Translocation and mutant ros kinase in human non-small cell lung carcinoma

ABSTRACT

In accordance with the invention, a novel gene translocation, (5q32, 6q22), in human non-small cell lung carcinoma (NSCLC) that results in a fusion proteins combining part of CD74 with Proto-oncogene Tyrosine Protein Kinase ROS Precursor (ROS) kinase has now been identified. The CD74-ROS fusion protein is anticipated to drive the proliferation and survival of a subgroup of NSCLC tumors. The invention therefore provides, in part, isolated polynucleotides and vectors encoding the disclosed mutant ROS kinase polypeptides, probes for detecting it, isolated mutant polypeptides, recombinant polypeptides, and reagents for detecting the fusion and truncated polypeptides. The disclosed identification of the new fusion protein enables new methods for determining the presence of these mutant ROS kinase polypeptides in a biological sample, methods for screening for compounds that inhibit the proteins, and methods for inhibiting the progression of a cancer characterized by the mutant polynucleotides or polypeptides, which are also provided by the invention.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.15/096,562, filed Apr. 12, 2016, which is a continuation of U.S. patentapplication Ser. No. 14/483,668, filed Sep. 11, 2014, now U.S. Pat. No.9,328,349, which is a divisional of U.S. patent Ser. No. 12/738,210,filed Apr. 15, 2010, now U.S. Pat. No. 9,096,855, which is a NationalStage Entry of International Application No. PCT/US2008/011968 filedOct. 20, 2008, which itself claims priority to U.S. ProvisionalApplication No. 60/999,668 Filed Oct. 18, 2007 now abandoned, the entirecontents of which are incorporated by reference herein.

INCORPORATION BY REFERENCE OF SEQUENCE LISTING

The Sequence Listing in the ASCII text file, named as28120AZY_CST_265_CON2_SequenceListing.txt of 44 KB, created on Nov. 18,2019, and submitted to the United States Patent and Trademark Office viaEFS-Web, is incorporated herein by reference.

FIELD OF THE INVENTION

The invention relates generally to proteins and genes involved incancer, and to the detection, diagnosis and treatment of cancer.

BACKGROUND OF THE INVENTION

Many cancers are characterized by disruptions in cellular signalingpathways that lead to aberrant control of cellular processes, or touncontrolled growth and proliferation of cells. These disruptions areoften caused by changes in the activity of particular signalingproteins, such as kinases. Among these cancers is non-small cell lungcarcinoma (NSCLC). NSCLC is the leading cause of cancer death in theUnited States, and accounts for about 87% of all lung cancers. There areabout 151,000 new cases of NSCLC in the United States annually, and itis estimated that over 120,000 patients will die annually from thedisease in the United States alone. See “Cancer Facts and Figures 2005.”American Cancer Society. NSCLC, which comprises three distinct subtypes,is often only detected after it has metastasized, and thus the mortalityrate is 75% within two years of diagnosis.

It is known that gene translocations resulting in kinase fusion proteinswith aberrant signaling activity can directly lead to certain cancers.For example, it has been directly demonstrated that the BCR-ABLoncoprotein, a tyrosine kinase fusion protein, is the causative agent inhuman chronic myelogenous leukemia (CML). The BCR-ABL oncoprotein, whichis found in at least 90-95% of CML cases, is generated by thetranslocation of gene sequences from the c-ABL protein tyrosine kinaseon chromosome 9 into BCR sequences on chromosome 22, producing theso-called Philadelphia chromosome. See, e.g. Kurzock et al., N. Engl. J.Med. 319: 990-998 (1988). The translocation is also observed in acutelymphocytic leukemia and AML cases.

Gene translocations leading to mutant or fusion proteins implicated in avariety of other cancers have been described. For example, Falini etal., Blood 99(2): 409-426 (2002), review translocations known to occurin hematological cancers. To date, only a limited number of genetranslocations and mutant proteins occurring in lung cancers have beendescribed, including the t(15;19) translocation involving Notch3. SeeDang et al., J. Natl. Can. Instit. 92(16): 1355-1357 (2000). Defects inRNA Binding Protein-6 (RBM-6) expression and/or activity have been foundin small cell and non-small cell lung carcinomas. See Drabkin et al.,Oncogene 8(16): 2589-97 (1999). However, to date, no translocations inhuman NSCLC cancer that involve protein kinases have been described.

CD74 is an integral membrane protein that functions as a MHC class IIchaperone protein. Defects in ROS kinase expression resulting from theFIG-ROS del(6)(q21.q21) translocation in glioblastoma have beendescribed. See Charest et al., Genes Chromos. Canc. 37(1): 58-71 (2003).A truncated form of ROS kinase able to drive tumor growth in mice hasalso been described. See Birchmeier et al., Mol. Cell. Bio. 6(9):3109-3115 (1986). To date, there are no known activating point mutationsthat occur in ROS kinase.

Identifying translocations and mutations in human cancers is highlydesirable because it can lead to the development of new therapeuticsthat target such fusion or mutant proteins, and to new diagnostics foridentifying patients that have such gene translocations. For example,BCR-ABL has become a target for the development of therapeutics to treatleukemia. Most recently, Gleevec® (Imatinib mesylate, STI-571), a smallmolecule inhibitor of the ABL kinase, has been approved for thetreatment of CML. This drug is the first of a new class ofanti-proliferative agents designed to interfere with the signalingpathways that drive the growth of tumor cells. The development of thisdrug represents a significant advance over the conventional therapiesfor CML and ALL, chemotherapy and radiation, which are plagued by wellknown side-effects and are often of limited effect since they fail tospecifically target the underlying causes of the malignancies. Likewise,reagents and methods for specifically detecting BCR-ABL fusion proteinin patients, in order to identify patients most likely to respond totargeted inhibitors like Gleevec®, have been described.

Accordingly, there remains a need for the identification of novel genetranslocations or mutations resulting in fusion or mutant proteinsimplicated in the progression of human cancers, including lung cancerslike NSCLC, and the development of new reagents and methods for thestudy and detection of such fusion proteins. Identification of suchfusion proteins will, among other things, desirably enable new methodsfor selecting patients for targeted therapies, as well as for thescreening of new drugs that inhibit such mutant/fusion proteins.

SUMMARY OF THE INVENTION

In accordance with the invention, a novel gene translocation. (5q32,6q22), in human non-small cell lung carcinoma (NSCLC) that results infusion proteins combining part of CD74 with Proto-Oncogene TyrosineProtein Kinase ROS precursor (ROS) kinase have now been identified. TheCD74-ROS fusion proteins are expected to retain ROS tyrosine kinaseactivity and to drive the proliferation and survival of NSCLC in asubset of such cancers in which the fusion protein is expressed.

The invention therefore provides, in part, isolated polynucleotides andvectors encoding the disclosed mutant ROS polypeptides, probes andassays for detecting them, isolated mutant ROS polypeptides, recombinantmutant polypeptides, and reagents for detecting the mutant ROSpolynucleotides and polypeptides. The disclosed identification of thenew mutant ROS kinase proteins and CD74 translocation enables newmethods for determining the presence of mutant ROS polynucleotides orpolypeptides in a biological sample, methods for screening for compoundsthat inhibit the mutant kinase proteins, and methods for inhibiting theprogression of a cancer characterized by the expression of mutant ROSpolynucleotides or polypeptides, which are also provided by theinvention. The aspects and embodiments of the invention are described inmore detail below.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1—shows the location of the CD74 gene and ROS gene on chromosomes5q and 6q respectively (panel A), and the domain locations of fulllength CD74 and ROS proteins as well as those CD74-ROS fusion protein(panels B and C). The fusion junction occurs at residue 1853 upstream ofthe transmembrane domain of ROS.

FIG. 2—is the amino acid sequence (1 letter code) of the human CD74-ROSfusion protein (SEQ ID NO: 1) (top panel) with coding DNA sequence alsoindicated (SEQ ID NO: 2) (bottom panel); the residues of the CD74 moietyare underlined, while the residues of the kinase domain of ROS are inbold.

FIG. 3—is the amino acid sequence (1 letter code) of human CD74 protein(SEQ ID NO: 3) (SwissProt Accession No. P04233) (top panel) with codingDNA sequence also indicated (SEQ ID NO: 4) (GeneBank Accession No.NM_001025159) (bottom panel); the residues involved in the translocationare underlined.

FIG. 4A—is the amino acid sequence (1 letter code) of human ROS kinase(SEQ ID NO: 5) (SwissProt Accession No. P08922); the residues involvedin the translocation are underlined.

FIG. 4B—is the coding DNA sequence of human ROS kinase (SEQ ID NO: 6)(GeneBank Accession No. NM_002944); the residues involved in thetranslocation are underlined.

FIG. 5—is the gel depicting the detection of the fusion gene formed bythe CD74 and ROS translocation by RT-PCR; with primer sequences shownfor CD74-F1 (top) and ROS-GSP3 (bottom) (SEQ ID NOs: 9 and 10,respectively).

FIG. 6—is an image showing specific detection of the ROSfusion/translocation (in a human NSCLC cell line and patient) by FISHusing a 2-color break-a-part probe

DETAILED DESCRIPTION OF THE INVENTION

In accordance with the invention, a previously unknown genetranslocation that results in a mutant kinase fusion protein. CD74-ROS,has now been identified in human non-small cell lung carcinoma (NSCLC),a subtype of lung carcinoma. The translocation, which occurs betweenchromosome (5q32) and chromosome (6q22), produces a fusion protein thatcombines the N-terminus of CD74, with the transmembrane and kinasedomains of Proto-Oncogene Tyrosine Protein Kinase ROS precursor (ROS)kinase, a 2347 amino acid receptor tyrosine kinase. The resultingCD74-ROS fusion protein, a 703 amino acid protein, is expected to retainkinase activity and to drive the proliferation and survival of a subsetof human NSCLC tumors in which the fusion protein is expressed.

Although a few gene translocations that result in aberrant fusionproteins involving ROS kinase have been described, including the FIG-ROSdel(6)(q21,q21) translocation in glioblastoma (see Charest et al.,(2003), supra.) and a truncated, active form of ROS (see Birchmeier etal., supra.), the presently disclosed CD74-ROS translocation and fusionprotein is novel, and this fusion kinase is the first reported inprimary human NSCLC patient. CD74 is an integral membrane protein thatfunctions as a MHC class II chaperone protein. ROS is a transmembranereceptor tyrosine kinase that belongs to the insulin receptor subfamily,and is involved in cell proliferation and differentiation processes. ROSis expressed, in humans, in epithelial cells of a variety of differenttissues. Defects in ROS expression and/or activation have been found inglioblastoma, as well as tumors of the central nervous system. See e.g.Charest et al. (2003), supra.

As further described below, the CD74-ROS translocation gene and fusionprotein have presently been isolated and sequenced, and cDNAs forexpressing the mutant kinase protein produced. Accordingly, theinvention provides, in part, isolated polynucleotides that encodeCD74-ROS fusion polypeptides, nucleic acid probes that hybridize to suchpolynucleotides, and methods, vectors, and host cells for utilizing suchpolynucleotides to produce recombinant mutant ROS polypeptides. Theinvention also provides, in part, isolated polypeptides comprising aminoacid sequences encoding CD74-ROS fusion polypeptides, recombinant mutantpolypeptides, and isolated reagents that specifically bind to and/ordetect CD74-ROS fusion polypeptides, but do not bind to or detect eitherwild type CD74 or wild type ROS. These aspects of the invention, whichare described in further detail below, will be useful, inter alia, infurther studying the mechanisms of cancers driven by mutant ROS kinaseexpression/activity, for identifying lung carcinomas and other cancerscharacterized by the CD74-ROS translocation and/or fusion proteins, andin practicing methods of the invention as further described below.

The identification of the novel ROS kinase mutants and translocation hasimportant implications for the potential diagnosis and treatment ofdiseases, such as NSCLC, that are characterized by this translocationand/or fusion protein. NSCLC is the leading cause of cancer death in theUnited States, and is often difficult to diagnose until after it hasmetastasized, increasing the difficulty of effectively treating orcuring this disease. The mortality rate of NSCLC is therefore 75% withintwo years of diagnosis. See American Cancer Society, supra. Althoughtargeted EGFR-inhibitors are presently approved for the treatment ofNSCLC, it is anticipated that this therapy may be partially or whollyineffective against those patients having tumors in which mutant ROSkinase (rather than or in addition to EGFR) is expressed and driving thedisease, in whole or in part.

Therefore, the present discovery of the CD74-ROS fusion proteinsresulting from gene translocation in NSCLC, which is expected to driveproliferation and survival in a subset of NSCLC tumors, enablesimportant new methods for accurately identifying mammalian lung cancers(such as NSCLC), as well as other cancers, in which CD74-ROS fusionprotein or truncated ROS kinase is expressed. These tumors are mostlikely to respond to inhibitors of the kinase activity of the mutant ROSkinases. The ability to identify, as early as possible, cancers that aredriven by a mutant ROS kinase will greatly assist in clinicallydetermining which therapeutic, or combination of therapeutics, will bemost appropriate for a particular patient, thus helping to avoidprescription of inhibitors targeting other kinases that are not, infact, the primary signaling molecule driving the cancer.

Accordingly, the invention provides, in part, methods for detecting thepresence of a CD74-ROS translocation (t(5,6)(q32, q22) and/or fusionpolypeptide in a cancer using fusion-specific and mutant-specificreagents of the invention. Such methods may be practiced, for example,to identify a cancer, such as a NSCLC tumor, that is likely to respondto an inhibitor of the ROS kinase activity of the mutant protein. Theinvention also provides, in part, methods for determining whether acompound inhibits the progression of a cancer characterized by aCD74-ROS fusion polypeptide. Further provided by the invention is amethod for inhibiting the progression of a cancer that expresses aCD74-ROS fusion polypeptide by inhibiting the expression and/or activityof the mutant polypeptide. Such methods are described in further detailbelow. Any suitable materials and/or methods known to those of skill canbe utilized in carrying out the present invention. However, preferredmaterials and methods are described. Materials, reagents and the like towhich reference is made in the following description and examples areobtainable from commercial sources, unless otherwise noted.

The further aspects, advantages, and embodiments of the invention aredescribed in more detail below. The patents, published applications, andscientific literature referred to herein establish the knowledge ofthose with skill in the art and are hereby incorporated by reference intheir entirety to the same extent as if each was specifically andindividually indicated to be incorporated by reference. Any conflictbetween any reference cited herein and the specific teachings of thisspecification shall be resolved in favor of the latter. Likewise, anyconflict between an art-understood definition of a word or phrase and adefinition of the word or phrase as specifically taught in thisspecification shall be resolved in favor of the latter. As used herein,the following terms have the meanings indicated. As used in thisspecification, the singular forms “a,” “an” and “the” specifically alsoencompass the plural forms of the terms to which they refer, unless thecontent clearly dictates otherwise. The term “about” is used herein tomean approximately, in the region of, roughly, or around. When the term“about” is used in conjunction with a numerical range, it modifies thatrange by extending the boundaries above and below the numerical valuesset forth. In general, the term “about” is used herein to modify anumerical value above and below the stated value by a variance of 20%.

“Antibody” or “antibodies” refers to all types of immunoglobulins,including IgG, IgM, IgA, IgD, and IgE, including F_(ab) orantigen-recognition fragments thereof, including chimeric, polyclonal,and monoclonal antibodies. Peptide antigens suitable for producingantibodies of the invention may be designed, constructed and employed inaccordance with well-known techniques. See, e.g., ANTIBODIES: ALABORATORY MANUAL, Chapter 5, p. 75-76. Harlow & Lane Eds., Cold SpringHarbor Laboratory (1988); Czernik, Methods In Enzymology, 201: 264-283(1991); Merrifield, J. Am. Chem. Soc. 85: 21-49 (1962)). Also within theinvention are antibody molecules with fewer than 4 chains, includingsingle chain antibodies. Camelid antibodies and the like and componentsof the antibody, including a heavy chain or a light chain. In someembodiments an immunoglobulin chain may comprise in order from 5′ to 3′,a variable region and a constant region. The variable region maycomprise three complementarity determining regions (CDRs), withinterspersed framework (FR) regions for a structure FR1, CDR1, FR2,CDR2, FR3, CDR3 and FR4. Also within the invention are heavy or lightchain variable regions, framework regions and CDRs. An antibody of theinvention may comprise a heavy chain constant region that comprises someor all of a CH1 region, hinge, CH2 and CH3 region. An antibody of theinvention may have an binding affinity (K_(D)) of 1×10⁻⁷ M or less. Inother embodiments, the antibody binds with a K_(D) of 1×10⁻⁸ M, 1×10⁻⁹M, 1×10⁻¹⁰ M, 1×10⁻¹¹ M, 1×10⁻¹²M or less. In certain embodiments, theK_(D) is 1 pM to 500 pM, between 500 pM to 1 μM, between 1 μM to 100 nM,or between 100 mM to 10 nM. Antibodies of the invention can be derivedfrom any species of animal, preferably a mammal. Non-limiting exemplarynatural antibodies include antibodies derived from human, chicken,goats, and rodents (e.g., rats, mice, hamsters and rabbits), includingtransgenic rodents genetically engineered to produce human antibodies(see, e.g., Lonberg et al., WO93/12227; U.S. Pat. No. 5,545,806; andKucherlapati, et al., WO91/10741; U.S. Pat. No. 6,150,584, which areherein incorporated by reference in their entirety). Natural antibodiesare the antibodies produced by a host animal, however the inventioncontemplates also genetically altered antibodies wherein the amino acidsequence has been varied from that of a native antibody. Because of therelevance of recombinant DNA techniques to this application, one neednot be confined to the sequences of amino acids found in naturalantibodies; antibodies can be redesigned to obtain desiredcharacteristics. The possible variations are many and range from thechanging of just one or a few amino acids to the complete redesign of,for example, the variable or constant region. Changes in the constantregion will, in general, be made in order to improve or altercharacteristics, such as complement fixation, interaction with membranesand other effector functions. Changes in the variable region will bemade in order to improve the antigen binding characteristics. The term“humanized antibody”, as used herein, refers to antibody molecules inwhich amino acids have been replaced in the non-antigen binding regionsin order to more closely resemble a human antibody, while stillretaining the original binding ability. Other antibodies specificallycontemplated are oligoclonal antibodies. As used herein, the phrase“oligoclonal antibodies” refers to a predetermined mixture of distinctmonoclonal antibodies. See, e.g., PCT publication WO 95/20401; U.S. Pat.Nos. 5,789,208 and 6,335,163. In one embodiment, oligoclonal antibodiesconsisting of a predetermined mixture of antibodies against one or moreepitopes are generated in a single cell. In other embodiments,oligoclonal antibodies comprise a plurality of heavy chains capable ofpairing with a common light chain to generate antibodies with multiplespecificities (e.g., PCT publication WO 04/009618). Oligoclonalantibodies are particularly useful when it is desired to target multipleepitopes on a single target molecule. In view of the assays and epitopesdisclosed herein, those skilled in the art can generate or selectantibodies or mixtures of antibodies that are applicable for an intendedpurpose and desired need. Recombinant antibodies against thephosphorylation sites identified in the invention are also included inthe present application. These recombinant antibodies have the sameamino acid sequence as the natural antibodies or have altered amino acidsequences of the natural antibodies in the present application. They canbe made in any expression systems including both prokaryotic andeukaryotic expression systems or using phage display methods (see, e.g.,Dower et al., WO91/17271 and McCafferty et al., WO92/01047; U.S. Pat.No. 5,969,108, which are herein incorporated by reference in theirentirety). Antibodies can be engineered in numerous ways. They can bemade as single-chain antibodies (including small modularimmunopharmaceuticals or SMIPs™), Fab and F(ab′)₂ fragments, etc.Antibodies can be humanized, chimerized, deimmunized, or fully human.Numerous publications set forth the many types of antibodies and themethods of engineering such antibodies. For example, see U.S. Pat. Nos.6,355,245; 6,180,370; 5,693,762; 6,407,213; 6,548,640; 5,565,332;5,225,539; 6,103,889; and 5,260,203. The genetically altered antibodiesshould be functionally equivalent to the above-mentioned naturalantibodies. In certain embodiments, modified antibodies provide improvedstability or/and therapeutic efficacy. Examples of modified antibodiesinclude those with conservative substitutions of amino acid residues,and one or more deletions or additions of amino acids that do notsignificantly deleteriously alter the antigen binding utility.Substitutions can range from changing or modifying one or more aminoacid residues to complete redesign of a region as long as thetherapeutic utility is maintained. Antibodies of this application can bemodified post-translationally (e.g., acetylation, and/orphosphorylation) or can be modified synthetically (e.g., the attachmentof a labeling group). Antibodies with engineered or variant constant orFc regions can be useful in modulating effector functions, such as, forexample, antigen-dependent cytotoxicity (ADCC) and complement-dependentcytotoxicity (CDC). Such antibodies with engineered or variant constantor Fc regions may be useful in instances where a parent singling protein(Table 1) is expressed in normal tissue; variant antibodies withouteffector function in these instances may elicit the desired therapeuticresponse while not damaging normal tissue. Accordingly, certain aspectsand methods of the present disclosure relate to antibodies with alteredeffector functions that comprise one or more amino acid substitutions,insertions, and/or deletions. The term “biologically active” refers to aprotein having structural, regulatory, or biochemical functions of anaturally occurring molecule. Likewise. “immunologically active” refersto the capability of the natural, recombinant, or synthetic CD74-ROSfusion polypeptide or truncated ROS polypeptide, or any oligopeptidethereof, to induce a specific immune response in appropriate animals orcells and to bind with specific antibodies.

The term “biological sample” is used in its broadest sense, and meansany biological sample suspected of containing CD74-ROS fusion ortruncated ROS polynucleotides or polypeptides or fragments thereof, andmay comprise a cell, chromosomes isolated from a cell (e.g., a spread ofmetaphase chromosomes), genomic DNA (in solution or bound to a solidsupport such as for Southern analysis). RNA (in solution or bound to asolid support such as for northern analysis), cDNA (in solution or boundto a solid support), an extract from cells, blood, urine, marrow, or atissue, and the like.

Technical and scientific terms used herein have the meaning commonlyunderstood by one of skill in the art to which the present inventionpertains, unless otherwise defined. Reference is made herein to variousmethodologies and materials known to those of skill in the art. Standardreference works setting forth the general principles of recombinant DNAtechnology include Sambrook et al., Molecular Cloning: A LaboratoryManual, 2nd Ed., Cold Spring Harbor Laboratory Press, New York (1989):Kaufman et al., Eds., Handbook of Molecular and Cellular Methods inBiology in Medicine. CRC Press, Boca Raton (1995); McPherson, Ed.,Directed Mutagenesis: A Practical Approach, IRL Press, Oxford (1991).Standard reference works setting forth the general principles ofpharmacology include Goodman and Gilman's The Pharmacological Basis ofTherapeutics, 11th Ed., McGraw Hill Companies Inc., New York (2006).

“Characterized by” with respect to a cancer and mutant ROSpolynucleotide or polypeptide is meant a cancer in which the CD74-ROSgene translocation and/or expressed fusion polypeptide are present, ascompared to a cancer in which such translocation and/or fusionpolypeptide are not present. The presence of such fusion polypeptide maydrive, in whole or in part, the growth and survival of such cancer.

“Consensus” refers to a nucleic acid sequence which has beenre-sequenced to resolve uncalled bases, or which has been extended usingXL-PCR™ (Perkin Elmer. Norwalk, Conn.) in the 5′ and/or the 3′ directionand re-sequenced, or which has been assembled from the overlappingsequences of more than one Incyte clone using the GELVIEW™ FragmentAssembly system (GCG, Madison, Wis.), or which has been both extendedand assembled.

“ROS kinase-inhibiting therapeutic” means any composition comprising oneor more compounds, chemical or biological, which inhibits, eitherdirectly or indirectly, the expression and/or activity of wild type ortruncated ROS, either alone and/or as part of the CD74-ROS fusionproteins.

“Derivative” refers to the chemical modification of a nucleic acidsequence encoding CD74-ROS fusion polypeptide or the encoded polypeptideitself. Illustrative of such modifications would be replacement ofhydrogen by an alkyl, acyl, or amino group. A nucleic acid derivativewould encode a polypeptide that retains essential biologicalcharacteristics of the natural molecule.

“Detectable label” with respect to a polypeptide, polynucleotide, orreagent disclosed herein means a chemical, biological, or othermodification, including but not limited to fluorescence, mass, residue,dye, radioisotope, label, or tag modifications, etc., by which thepresence of the molecule of interest may be detected.

“Expression” or “expressed” with respect to CD74-ROS fusion polypeptidein a biological sample means significantly expressed as compared tocontrol sample in which this fusion polypeptide is not significantlyexpressed.

“Heavy-isotope labeled peptide” (used interchangeably with AQUA peptide)means a peptide comprising at least one heavy-isotope label, which issuitable for absolute quantification or detection of a protein asdescribed in WO/03016861, “Absolute Quantification of Proteins andModified Forms Thereof by Multistage Mass Spectrometry” (Gygi et al.),further discussed below. The term “specifically detects” with respect tosuch an AQUA peptide means the peptide will only detect and quantifypolypeptides and proteins that contain the AQUA peptide sequence andwill not substantially detect polypeptides and proteins that do notcontain the AQUA peptide sequence.

“Isolated” (or “substantially purified”) refers to nucleic or amino acidsequences that are removed from their natural environment, isolated orseparated. They preferably are at least 60% free, more preferably 75%free, and most preferably 90% or more free from other components withwhich they are naturally associated.

“Mimetic” refers to a molecule, the structure of which is developed fromknowledge of the structure of CD74-ROS fusion polypeptide or portionsthereof and, as such, is able to effect some or all of the actions oftranslocation associated protein-like molecules.

“Mutant ROS” polynucleotide or polypeptide means a CD74-ROS fusionpolynucleotide or polypeptide as described herein.

“Polynucleotide” (or “nucleotide sequence”) refers to anoligonucleotide, nucleotide, or polynucleotide, and fragments orportions thereof, and to DNA or RNA of genomic or synthetic origin,which may be single- or double-stranded, and represent the sense oranti-sense strand.

“Polypeptide” (or “amino acid sequence”) refers to an oligopeptide,peptide, polypeptide, or protein sequence, and fragments or portionsthereof, and to naturally occurring or synthetic molecules. Where “aminoacid sequence” is recited herein to refer to an amino acid sequence of anaturally occurring protein molecule, “amino acid sequence” and liketerms, such as “polypeptide” or “protein”, are not meant to limit theamino acid sequence to the complete, native amino acid sequenceassociated with the recited protein molecule.

“CD74-ROS fusion polynucleotide” refers to the nucleic acid sequence ofa substantially purified CD74-ROS translocation gene product or fusionpolynucleotide as described herein, obtained from any species,particularly mammalian, including bovine, ovine, porcine, murine,equine, and preferably human, from any source whether natural,synthetic, semi-synthetic, or recombinant.

“CD74-ROS fusion polypeptide” refers to the amino acid sequence of asubstantially purified CD74-ROS fusion polypeptide described herein,obtained from any species, particularly mammalian, including bovine,ovine, porcine, murine, equine, and preferably human, from any sourcewhether natural, synthetic, semi-synthetic, or recombinant.

The terms “specifically binds to” (or “specifically binding” or“specific binding”) in reference to the interaction of an antibody and aprotein or peptide, mean that the interaction is dependent upon thepresence of a particular structure (i.e., the antigenic determinant orepitope) on the protein; in other words, the antibody is recognizing andbinding to a specific protein structure rather than to proteins ingeneral. The term “does not bind” with respect to an antibody's bindingto sequences or antigenic determinants other than that for which it isspecific means does not substantially react with as compared to theantibody's binding to antigenic determinant or sequence for which theantibody is specific.

The term “stringent conditions” with respect to sequence or probehybridization conditions is the “stringency” that occurs within a rangefrom about T. minus 5° C. (5° C. below the melting temperature (T_(m))of the probe or sequence) to about 20° C., to 25° C., below T_(m).Typical stringent conditions are: overnight incubation at 42° C. in asolution comprising: 50% formamide, 5×SSC (750 mM NaCl, 75 mM trisodiumcitrate), 50 mM sodium phosphate (pH 7.6), 5×Denhardt's solution, 10%dextran sulfate, and 20 micrograms/ml denatured, sheared salmon spermDNA, followed by washing the filters in 0. IX SSC at about 65° C. Aswill be understood by those of skill in the art, the stringency ofhybridization may be altered in order to identify or detect identical orrelated polynucleotide sequences.

A “variant” of CD74-ROS fusion polypeptide refers to an amino acidsequence that is altered by one or more amino acids. The variant mayhave “conservative” changes, wherein a substituted amino acid hassimilar structural or chemical properties. e.g., replacement of leucinewith isoleucine. More rarely, a variant may have “nonconservative”changes, e.g., replacement of a glycine with a tryptophan. Similar minorvariations may also include amino acid deletions or insertions, or both.Guidance in determining which amino acid residues may be substituted,inserted, or deleted without abolishing biological or immunologicalactivity may be found using computer programs well known in the art, forexample, DNASTAR software.

A. Identification Mutant ROS Kinase in Human NSCLC.

The novel human gene translocation disclosed herein, which occursbetween chromosome (5q32) and chromosome (6q22) in human NSCLC andresults in expression of two variant fusion proteins that combine theN-terminus (exons 1-6) of CD74 with the transmembrane and kinase domains(exons 34-43) of ROS, was surprisingly identified during examination ofglobal phosphorylated peptide profiles in extracts from a humannon-small cell lung carcinoma (NSCLC) patient, a subtype of lungcancers. The chromosomes, genes, and product involved in thistranslocation are shown in FIG. 1.

The phosphorylation profile of this cell line was elucidated using arecently described technique for the isolation and mass spectrometriccharacterization of modified peptides from complex mixtures (see U.S.Patent Publication No. 20030044848, Rush et al., “ImmunoaffinityIsolation of Modified Peptides from Complex Mixtures” (the “IAP”technique), as further described in Example 1 herein. Application of theIAP technique using a phosphotyrosine-specific antibody (CELL SIGNALINGTECHNOLOGY, INC., Beverly, Mass., 2003/04 Cat. #9411), identified thatthe a NSCLC patient expresses ROS kinase (in contrast to most of theother NSCLC patients, which do not). The screen identified many otheractivated kinases in this patient including ROS. Analysis of thesequence 5′ to ROS by 5′ RACE then identified that the kinase was fusedto the N-terminus of CD74 (see FIG. 5).

As shown in panel B of FIG. 1, the CD74-ROS translocation combines theN-terminus of CD74 (amino acids 1-208) with the transmembrane and kinasedomains of ROS (amino acids 1853-2347) (see also SEQ ID NOs:1), toproduce a fusion (see panel C of FIG. 1). The translocation retains the5′-most transmembrane domain of CD74. The resulting CD74-ROS fusionproteins, which comprise 703 amino acids. (see panel C of FIG. 1 andFIG. 2 (SEQ ID NOs: 1) and are expected to retain kinase activity ofROS.

Global phosphopeptide profiling and FISH analysis of human NSCLC tumorsindicate that a small percentage of patients do in fact harbor thismutation (see Examples 1 and 3), and these patients may benefit from ROSinhibitor therapy.

B. Isolated Polynucleotides.

The present invention provides, in part, isolated polynucleotides thatencode CD74-ROS fusion polypeptides, nucleotide probes that hybridize tosuch polynucleotides, and methods, vectors, and host cells for utilizingsuch polynucleotides to produce recombinant fusion polypeptides. Unlessotherwise indicated, all nucleotide sequences determined by sequencing aDNA molecule herein were determined using an automated DNA sequencer(such as the Model 373 from Applied Biosystems, Inc.), and all aminoacid sequences of polypeptides encoded by DNA molecules determinedherein were determined using an automated peptide sequencer. As is knownin the art for any DNA sequence determined by this automated approach,any nucleotide sequence determined herein may contain some errors.Nucleotide sequences determined by automation are typically at leastabout 90% identical, more typically at least about 95% to at least about99.9% identical to the actual nucleotide sequence of the sequenced DNAmolecule. The actual sequence can be more precisely determined by otherapproaches including manual DNA sequencing methods well known in theart. As is also known in the art, a single insertion or deletion in adetermined nucleotide sequence compared to the actual sequence willcause a frame shift in translation of the nucleotide sequence such thatthe predicted amino acid sequence encoded by a determined nucleotidesequence will be completely different from the amino acid sequenceactually encoded by the sequenced DNA molecule, beginning at the pointof such an insertion or deletion. Unless otherwise indicated, eachnucleotide sequence set forth herein is presented as a sequence ofdeoxyribonucleotides (abbreviated A, G, C and T). However, by“nucleotide sequence” of a nucleic acid molecule or polynucleotide isintended, for a DNA molecule or polynucleotide, a sequence ofdeoxyribonucleotides, and for an RNA molecule or polynucleotide, thecorresponding sequence of ribonucleotides (A, G, C and U), where eachthymidine deoxyribonucleotide (T) in the specified deoxyribonucleotidesequence is replaced by the ribonucleotide uridine (U). For instance,reference to an RNA molecule having the sequence of SEQ ID NOs: 2 or setforth using deoxyribonucleotide abbreviations is intended to indicate anRNA molecule having a sequence in which each deoxyribonucleotide A, G orC of SEQ ID NOs: 2 has been replaced by the corresponding ribonucleotideA, G or C, and each deoxyribonucleotide T has been replaced by aribonucleotide U.

In one embodiment, the invention provides an isolated polynucleotidecomprising a nucleotide sequence at least 95% identical to a sequenceselected from the group consisting of: (a) a nucleotide sequenceencoding a CD74-ROS fusion polypeptide comprising the amino acidsequence of SEQ ID NO: 1; (b) a nucleotide sequence encoding a CD74-ROSfusion polypeptide comprising the N-terminal amino acid sequence of CD74(residues 1-208 of SEQ ID NO: 3) and the kinase domain of ROS (residues1945-2222 of SEQ ID NO: 5); (c) a nucleotide sequence comprising theN-terminal nucleotide sequence of CD74 (residues 1-624 of SEQ ID NO: 4)and the kinase domain nucleotide sequence of ROS (residues 6032-6865 ofSEQ ID NO: 6); (d) a nucleotide sequence comprising at least sixcontiguous nucleotides encompassing the fusion junction (residues622-627 of SEQ ID NO: 2) of a CD74-ROS fusion polynucleotide; (e) anucleotide sequence encoding a polypeptide comprising at least sixcontiguous amino acids encompassing the fusion junction (residues208-209 of SEQ ID NO: 1 of a CD74-ROS fusion polypeptide; and (f) anucleotide sequence complementary to any of the nucleotide sequences of(a)-(e).

Using the information provided herein, such as the nucleotide sequencesin FIG. 2 (SEQ ID NOs: 2), a nucleic acid molecule of the presentinvention encoding a mutant ROS polypeptide of the invention may beobtained using standard cloning and screening procedures, such as thosefor cloning cDNAs using mRNA as starting material. The fusion gene canalso be identified in cDNA libraries in other lung carcinomas or cancersin which the CD74-ROS translocation (5q32, 6q22) occurs, or in which adeletion or alternative translocation results in expression of atruncated ROS kinase lacking the extracellular domain of the wild typekinase.

The determined nucleotide sequence of the CD74-ROS translocation geneproducts (SEQ ID NO: 2) encode kinase fusion protein 703 amino acids(see FIG. 2 (SEQ ID NO: 1) and FIG. 1). The CD74-ROS fusionpolynucleotides comprise the portion of the nucleotide sequence of wildtype CD74 (see FIG. 3 (SEQ ID NO: 3) that encodes the N-terminus of thatprotein (exons 1-6) with the portion of the nucleotide sequence of wildtype ROS (see FIG. 4 (SEQ ID NO: 5) that encodes the transmembrane andkinase domains of that protein (exons 34-43). See FIG. 1.

As indicated, the present invention provides, in part, the mature formof the CD74-ROS fusion proteins. According to the signal hypothesis,proteins secreted by mammalian cells have a signal or secretory leadersequence which is cleaved from the mature protein once export of thegrowing protein chain across the rough endoplasmic reticulum has beeninitiated. Most mammalian cells and even insect cells cleave secretedproteins with the same specificity. However, in some cases, cleavage ofa secreted protein is not entirely uniform, which results in two or moremature species on the protein. Further, it has long been known that thecleavage specificity of a secreted protein is ultimately determined bythe primary structure of the complete protein, that is, it is inherentin the amino acid sequence of the polypeptide. Therefore, the presentinvention provides, in part, nucleotide sequences encoding a matureCD74-ROS fusion polypeptide having the amino acid sequence encoded bythe cDNA clone, which was deposited with the American Type CultureCollection (Manassas, Va., U.S.A.) on Sep. 20, 2006 in accordance withthe provisions of the Budapest Treaty.

By the mature CD74-ROS polypeptide having the amino acid sequenceencoded by the deposited cDNA clone is meant the mature form of thisfusion protein produced by expression in a mammalian cell (e.g., COScells, as described below) of the complete open reading frame encoded bythe human DNA sequence of the clone contained in the vector in thedeposited host cell.

As indicated, polynucleotides of the present invention may be in theform of RNA, such as mRNA, or in the form of DNA, including, forinstance, cDNA and genomic DNA obtained by cloning or producedsynthetically. The DNA may be double-stranded or single-stranded.Single-stranded DNA or RNA may be the coding strand, also known as thesense strand, or it may be the non-coding strand, also referred to asthe anti-sense strand.

Isolated polynucleotides of the invention are nucleic acid molecules,DNA or RNA, which have been removed from their native environment. Forexample, recombinant DNA molecules contained in a vector are consideredisolated for the purposes of the present invention. Further examples ofisolated DNA molecules include recombinant DNA molecules maintained inheterologous host cells or purified (partially or substantially) DNAmolecules in solution. Isolated RNA molecules include in vivo or invitro RNA transcripts of the DNA molecules of the present invention.Isolated nucleic acid molecules according to the present inventionfurther include such molecules produced synthetically.

Isolated polynucleotides of the invention include the DNA moleculesshown in FIG. 2 (SEQ ID NOs: 2), DNA molecules comprising the codingsequence for the mature CD74-ROS fusion proteins shown in FIG. 1 (SEQ IDNOs: 1), and DNA molecules that comprise a sequence substantiallydifferent from those described above but which, due to the degeneracy ofthe genetic code, still a mutant ROS polypeptide of the invention. Thegenetic code is well known in the art, thus, it would be routine for oneskilled in the art to generate such degenerate variants.

In another embodiment, the invention provides an isolated polynucleotideencoding the CD74-ROS fusion polypeptide comprising the CD74-ROStranslocation nucleotide sequence contained in the above-describeddeposited cDNA clone. Preferably, such nucleic acid molecule will encodethe mature fusion polypeptide encoded by the deposited cDNA clone. Inanother embodiment, the invention provides an isolated nucleotidesequence encoding a CD74-ROS fusion polypeptide comprising theN-terminal amino acid sequence of CD74 (residues 1-208 of SEQ ID NO: 3)and the kinase domain of ROS (residues 1945-2222 of SEQ ID NO: 5). Inone embodiment, the polypeptide comprising the kinase domain of ROScomprises residues 1853-2347 of SEQ ID NO: 5 (see FIG. 1, panel B). Inanother embodiment, the aforementioned N-terminal amino acid sequence ofCD74 and kinase domain of ROS are encoded by nucleotide sequencescomprising nucleotides 1-624 of SEQ ID NO: 4 and nucleotides 6032-6865of SEQ ID NO: 6, respectively.

The invention further provides isolated polynucleotides comprisingnucleotide sequences having a sequence complementary to one of themutant ROS fusion polypeptides of the invention. Such isolatedmolecules, particularly DNA molecules, are useful as probes for genemapping, by in situ hybridization with chromosomes, and for detectingexpression of the CD74-ROS fusion protein or truncated ROS kinasepolypeptide in human tissue, for instance, by Northern blot analysis.

The present invention is further directed to fragments of the isolatednucleic acid molecules described herein. By a fragment of an isolatedCD74-ROS polynucleotide or truncated ROS polynucleotide of the inventionis intended fragments at least about 15 nucleotides, and more preferablyat least about 20 nucleotides, still more preferably at least about 30nucleotides, and even more preferably, at least about 40 nucleotides inlength, which are useful as diagnostic probes and primers as discussedherein. Of course, larger fragments of about 50-1500 nucleotides inlength are also useful according to the present invention, as arefragments corresponding to most, if not all, of the CD74-ROS nucleotidesequence of the deposited cDNA or as shown in FIG. 2 (SEQ ID NOs: 2). Bya fragment at least 20 nucleotides in length, for example, is intendedfragments that include 20 or more contiguous bases from the respectivenucleotide sequences from which the fragments are derived.

Generation of such DNA fragments is routine to the skilled artisan, andmay be accomplished, by way of example, by restriction endonucleasecleavage or shearing by sonication of DNA obtainable from the depositedcDNA clone or synthesized according to the sequence disclosed herein.Alternatively, such fragments can be directly generated synthetically.

Preferred nucleic acid fragments or probes of the present inventioninclude nucleic acid molecules encoding the fusion junction of theCD74-ROS translocation gene products (see FIG. 1, panels B and C). Forexample, in certain preferred embodiments, an isolated polynucleotide ofthe invention comprises a nucleotide sequence/fragment comprising atleast six contiguous nucleotides encompassing the fusion junction(residues 622-627 of SEQ ID NO: 2) of a CD74-ROS fusion polynucleotide.In another preferred embodiment, an isolated polynucleotide of theinvention comprises a nucleotide sequence/fragment that encodes apolypeptide comprising at least six contiguous amino acids encompassingthe fusion junction (residues 208-209 of SEQ ID NO: 1) of a CD74-ROSfusion polypeptide.

In another aspect, the invention provides an isolated polynucleotidethat hybridizes under stringent hybridization conditions to a portion ofan mutant ROS kinase polynucleotide of the invention as describedherein. By “stringent hybridization conditions” is intended overnightincubation at 42° C. in a solution comprising: 50% formamide, 5×SSC (750mM NaCl, 75 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6),5×Denhardt's solution, 10% dextran sulfate, and 20 micrograms/mldenatured, sheared salmon sperm DNA, followed by washing the filters in0.1×SSC at about 65° C.

By a polynucleotide that hybridizes to a “portion” of a polynucleotideis intended a polynucleotide (either DNA or RNA) hybridizing to at leastabout 15 nucleotides (nt), and more preferably at least about 20 nt,still more preferably at least about 30 nt, and even more preferablyabout 30-70 nt of the reference polynucleotide. These are useful asdiagnostic probes and primers (e.g. for PCR) as discussed above and inmore detail below.

Of course, polynucleotides hybridizing to a larger portion of thereference polynucleotide (e.g. the mature CD74-ROS fusionpolynucleotides described in FIG. 2 (SEQ ID NOs: 2), for instance, aportion 50-750 nt in length, or even to the entire length of thereference polynucleotide, are also useful as probes according to thepresent invention, as are polynucleotides corresponding to most, if notall, of the nucleotide sequence of the deposited cDNA or the nucleotidesequences shown in FIG. 2 (SEQ ID NOs: 2).

By a portion of a polynucleotide of “at least 20 nucleotides in length,”for example, is intended 20 or more contiguous nucleotides from thenucleotide sequence of the reference polynucleotide. As indicated, suchportions are useful diagnostically either as a probe according toconventional DNA hybridization techniques or as primers foramplification of a target sequence by the polymerase chain reaction(PCR), as described, for instance, in MOLECULAR CLONING, A LABORATORYMANUAL, 2nd, edition, Sambrook, J., Fritsch. E. F. and Maniatis, T.,eds., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.(1989), the entire disclosure of which is hereby incorporated herein byreference. Of course, a polynucleotide which hybridizes only to a poly Asequence (such as the 3′ terminal poly(A) tract of the CD74-ROSsequences shown in FIG. 2 (SEQ ID NOs: 2) or to a complementary stretchof T (or U) resides, would not be included in a polynucleotide of theinvention used to hybridize to a portion of a nucleic acid of theinvention, since such a polynucleotide would hybridize to any nucleicacid molecule containing a poly (A) stretch or the complement thereof(e.g., practically any double-stranded cDNA clone).

As indicated, nucleic acid molecules of the present invention, whichencode a mutant ROS kinase polypeptide of the invention, may include butare not limited to those encoding the amino acid sequence of the maturepolypeptide, by itself: the coding sequence for the mature polypeptideand additional sequences, such as those encoding the leader or secretorysequence, such as a pre-, or pro- or pre-pro-protein sequence, thecoding sequence of the mature polypeptide, with or without theaforementioned additional coding sequences, together with additional,non-coding sequences, including for example, but not limited to intronsand non-coding 5′ and 3′ sequences, such as the transcribed,non-translated sequences that play a role in transcription, mRNAprocessing, including splicing and polyadenylation signals, forexample—ribosome binding and stability of mRNA; an additional codingsequence which codes for additional amino acids, such as those whichprovide additional functionalities.

Thus, the sequence encoding the polypeptide may be fused to a markersequence, such as a sequence encoding a peptide that facilitatespurification of the fused polypeptide. In certain preferred embodimentsof this aspect of the invention, the marker amino acid sequence is ahexa-histidine peptide, such as the tag provided in a pQE vector(Qiagen, Inc.), among others, many of which are commercially available.As described in Gentz et al., Proc. Natl. Acad. Sci. USA 86: 821-824(1989), for instance, hexa-histidine provides for convenientpurification of the fusion protein. The “HA” tag is another peptideuseful for purification which corresponds to an epitope derived from theinfluenza hemagglutinin protein, which has been described by Wilson etal., Cell 37: 767 (1984). As discussed below, other such fusion proteinsinclude the CD74-ROS fusion polypeptide itself fused to Fc at the N- orC-terminus.

The present invention further relates to variants of the nucleic acidmolecules of the present invention, which encode portions, analogs orderivatives of a CD74-ROS fusion polypeptide or truncated ROS kinasepolypeptide disclosed herein. Variants may occur naturally, such as anatural allelic variant. By an “allelic variant” is intended one ofseveral alternate forms of a gene occupying a given locus on achromosome of an organism. See, e.g. GENES II, Lewin, B., ed., JohnWiley & Sons, New York (1985). Non-naturally occurring variants may beproduced using art-known mutagenesis techniques.

Such variants include those produced by nucleotide substitutions,deletions or additions. The substitutions, deletions or additions mayinvolve one or more nucleotides. The variants may be altered in codingregions, non-coding regions, or both. Alterations in the coding regionsmay produce conservative or non-conservative amino acid substitutions,deletions or additions. Especially preferred among these are silentsubstitutions, additions and deletions, which do not alter theproperties and activities (e.g. kinase activity) of the mutant ROSkinase polypeptides disclosed herein. Also especially preferred in thisregard are conservative substitutions.

Further embodiments of the invention include isolated polynucleotidescomprising a nucleotide sequence at least 90/o identical. In someembodiments of the invention the nucleotide is at least 95%, 96%, 97%,98% or 99% identical, to a mutant ROS polynucleotide of the invention(for example, a nucleotide sequence encoding the RB-ROS fusionpolypeptide having the complete amino acid sequence shown in FIG. 2 (SEQID NOs: 1; or a nucleotide sequence encoding the N-terminal of CD74 andthe kinase domain of ROS (see FIG. 1, panel B; and FIGS. 3 and 4); or anucleotide complementary to such exemplary sequences).

By a polynucleotide having a nucleotide sequence at least, for example,95% “identical” to a reference nucleotide sequence encoding a mutant ROSkinase polypeptide is intended that the nucleotide sequence of thepolynucleotide is identical to the reference sequence except that thepolynucleotide sequence may include up to five point mutations per each100 nucleotides of the reference nucleotide sequence encoding the mutantROS polypeptide. In other words, to obtain a polynucleotide having anucleotide sequence at least 95% identical to a reference nucleotidesequence, up to 5% of the nucleotides in the reference sequence may bedeleted or substituted with another nucleotide, or a number ofnucleotides up to 5% of the total nucleotides in the reference sequencemay be inserted into the reference sequence. These mutations of thereference sequence may occur at the 5″ terminal positions of thereference nucleotide sequence or anywhere between those terminalpositions, interspersed either individually among nucleotides in thereference sequence or in one or more contiguous groups within thereference sequence.

As a practical matter, whether any particular nucleic acid molecule isat least 90%, 95%, 96%, 97%, 98% or 99% identical to, for instance, thenucleotide sequences shown in FIG. 2 (SEQ ID NOs: 2) or to thenucleotide sequence of the deposited cDNA clone described above can bedetermined conventionally using known computer programs such as theBestfit program (Wisconsin Sequence Analysis Package, Version 8 forUnix. Genetics Computer Group, University Research Park, 575 ScienceDrive, Madison. Wis. 53711. Bestfit uses the local homology algorithm ofSmith and Waterman, Advances in Applied Mathematics 2: 482-489 (1981),to find the best segment of homology between two sequences. When usingBestfit or any other sequence alignment program to determine whether aparticular sequence is, for instance, 95% identical to a referenceCD74-ROS fusion polynucleotide sequence according to the presentinvention, the parameters are set of course, such that the percentage ofidentity is calculated over the full length of the reference nucleotidesequence and that gaps in homology of up to 5% of the total number ofnucleotides in the reference sequence are allowed.

The present invention includes in its scope nucleic acid molecules atleast 90%, 95%, 96%, 97%, 98% or 99% identical to the nucleic acidsequences shown in FIG. 2 (SEQ ID NOs: 2), or to nucleotides 625-2172 ofSEQ ID NO: 2, or to the nucleic acid sequence of the deposited cDNA,irrespective of whether they encode a polypeptide having ROS kinaseactivity. This is because even where a particular nucleic acid moleculedoes not encode a fusion polypeptide having ROS kinase activity, one ofskill in the art would still know how to use the nucleic acid molecule,for instance, as a hybridization probe or a polymerase chain reaction(PCR) primer. Uses of the nucleic acid molecules of the presentinvention that do not encode a polypeptide having kinase include, interalia, (1) isolating the CD74-ROS translocation gene or allelic variantsthereof in a cDNA library; (2) in situ hybridization (e.g., “FISH”) tometaphase chromosomal spreads to provide precise chromosomal location ofthe CD74-ROS translocation gene, as described in Verma et al., HUMANCHROMOSOMES: A MANUAL OF BASIC TECHNIQUES, Pergamon Press, New York(1988); and Northern Blot analysis for detecting CD74-ROS fusion proteinmRNA expression in specific tissues.

Within the invention are also nucleic acid molecules having sequences atleast 95% identical to a mutant ROS kinase polypeptide of the inventionor to the nucleic acid sequence of the deposited cDNA, which do, infact, encode a fusion polypeptide having ROS kinase activity. Suchactivity may be similar, but not necessarily identical, to the activityof the CD74-ROS fusion protein disclosed herein (either the full-lengthprotein, the mature protein, or a protein fragment that retains kinaseactivity), as measured in a particular biological assay. For example,the kinase activity of ROS can be examined by determining its ability tophosphorylate one or more tyrosine containing peptide substrates, forexample, “Src-related peptide” (RRLIEDAEYAARG), which is a substrate formany receptor and nonreceptor tyrosine kinases.

Due to the degeneracy of the genetic code, one of ordinary skill in theart will immediately recognize that a large number of the nucleic acidmolecules having a sequence at least 90%, 95%, 96%, 97%, 98%, or 99%identical to the nucleic acid sequence of the deposited cDNA or thenucleic acid sequence shown in FIG. 2 (SEQ ID NOs: 2) will encode afusion polypeptide having ROS kinase activity. In fact, since degeneratevariants of these nucleotide sequences all encode the same polypeptide,this will be clear to the skilled artisan even without performing theabove described comparison assay. It will be further recognized in theart that, for such nucleic acid molecules that are not degeneratevariants, a reasonable number will also encode a polypeptide thatretains ROS kinase activity. This is because the skilled artisan isfully aware of amino acid substitutions that are either less likely ornot likely to significantly effect protein function (e.g., replacing onealiphatic amino acid with a second aliphatic amino acid). For example,guidance concerning how to make phenotypically silent amino acidsubstitutions is provided in Bowie et al., “Deciphering the Message inProtein Sequences: Tolerance to Amino Acid Substitutions.” Science 247:1306-1310 (1990), which describes two main approaches for studying thetolerance of an amino acid sequence to change. Skilled artisans familiarwith such techniques also appreciate which amino acid changes are likelyto be permissive at a certain position of the protein. For example, mostburied amino acid residues require nonpolar side chains, whereas fewfeatures of surface side chains are generally conserved. Other suchphenotypically silent substitutions are described in Bowie et al.,supra., and the references cited therein.

Methods for DNA sequencing that are well known and generally availablein the art may be used to practice any polynucleotide embodiments of theinvention. The methods may employ such enzymes as the Klenow fragment ofDNA polymerase 1, SEQUENASE® (US Biochemical Corp. Cleveland, Ohio). Taqpolymerase (Perkin Elmer), thermostable T7 polymerase (Amersham,Chicago, Ill.), or combinations of recombinant polymerases andproofreading exonucleases such as the ELONGASE Amplification Systemmarketed by Gibco BRL (Gaithersburg, Md.). Preferably, the process isautomated with machines such as the Hamilton Micro Lab 2200 (Hamilton,Reno, Nev.), Peltier Thermal Cycler (PTC200; MJ Research, Watertown,Mass.) and the ABI 377 DNA sequencers (Perkin Elmer).

Polynucleotide sequences encoding a mutant ROS polypeptide of theinvention may be extended utilizing a partial nucleotide sequence andemploying various methods known in the art to detect upstream sequencessuch as promoters and regulatory elements. For example, one method thatmay be employed. “restriction-site” PCR, uses universal primers toretrieve unknown sequence adjacent to a known locus (Sarkar, G., PCRMethods Applic. 2: 318-322 (1993)). In particular, genomic DNA is firstamplified in the presence of primer to linker sequence and a primerspecific to the known region. Exemplary primers are those described inExample 4 herein. The amplified sequences are then subjected to a secondround of PCR with the same linker primer and another specific primerinternal to the first one. Products of each round of PCR are transcribedwith an appropriate RNA polymerase and sequenced using reversetranscriptase.

Inverse PCR may also be used to amplify or extend sequences usingdivergent primers based on a known region (Triglia et al., Nucleic AcidsRes. 16: 8186 (1988)). The primers may be designed using OLIGO 4.06Primer Analysis software (National Biosciences Inc. Plymouth, Minn.), oranother appropriate program, to be 22-30 nucleotides in length, to havea GC content of 50% or more, and to anneal to the target sequence attemperatures about 68-72° C. The method uses several restriction enzymesto generate a suitable fragment in the known region of a gene. Thefragment is then circularized by intramolecular ligation and used as aPCR template.

Another method which may be used is capture PCR which involves PCRamplification of DNA fragments adjacent to a known sequence in human andyeast artificial chromosome DNA (Lagerstrom et al., PCR Methods Applic.1: 111-119 (1991)). In this method, multiple restriction enzymedigestions and ligations may also be used to place an engineereddouble-stranded sequence into an unknown portion of the DNA moleculebefore performing PCR. Another method which may be used to retrieveunknown sequences is that described in Parker et al., Nucleic Acids Res.19: 3055-3060 (1991)). Additionally, one may use PCR, nested primers,and PROMOTERFINDER® libraries to walk in genomic DNA (Clontech, PaloAlto, Calif.). This process avoids the need to screen libraries and isuseful in finding intron/exon junctions.

When screening for full-length cDNAs, it is preferable to use librariesthat have been size-selected to include larger cDNAs. Also,random-primed libraries are preferable, in that they will contain moresequences that contain the 5′ regions of genes. Use of a randomly primedlibrary may be especially preferable for situations in which an oligod(T) library does not yield a full-length cDNA. Genomic libraries may beuseful for extension of sequence into the 5′ and 3′ non-transcribedregulatory regions.

Capillary electrophoresis systems, which are commercially available, maybe used to analyze the size or confirm the nucleotide sequence ofsequencing or PCR products. In particular, capillary sequencing mayemploy flowable polymers for electrophoretic separation, four differentfluorescent dyes (one for each nucleotide) that are laser activated, anddetection of the emitted wavelengths by a charge coupled device camera.Output/light intensity may be converted to electrical signal usingappropriate software (e.g. GENOTYPER™ and SEQUENCE NAVIGATOR™, PerkinElmer) and the entire process from loading of samples to computeranalysis and electronic data display may be computer controlled.Capillary electrophoresis is especially preferable for the sequencing ofsmall pieces of DNA that might be present in limited amounts in aparticular sample.

C. Vectors and Host Cells.

The present invention also provides recombinant vectors that comprise anisolated polynucleotide of the present invention, host cells which aregenetically engineered with the recombinant vectors, and the productionof recombinant CD74-ROS polypeptides or fragments thereof by recombinanttechniques.

Recombinant constructs may be introduced into host cells usingwell-known techniques such infection, transduction, transfection,transvection, electroporation and transformation. The vector may be, forexample, a phage, plasmid, viral or retroviral vector. Retroviralvectors may be replication competent or replication defective. In thelatter case, viral propagation generally will occur only incomplementing host cells.

The polynucleotides may be joined to a vector containing a selectablemarker for propagation in a host. Generally, a plasmid vector isintroduced in a precipitate, such as a calcium phosphate precipitate, orin a complex with a charged lipid. If the vector is a virus, it may bepackaged in vitro using an appropriate packaging cell line and thentransduced into host cells. The invention may be practiced with vectorscomprising cis-acting control regions to the polynucleotide of interest.Appropriate trans-acting factors may be supplied by the host, suppliedby a complementing vector or supplied by the vector itself uponintroduction into the host. In certain preferred embodiments in thisregard, the vectors provide for specific expression, which may beinducible and/or cell type-specific (e.g., those inducible byenvironmental factors that are easy to manipulate, such as temperatureand nutrient additives).

The DNA insert comprising a CD74-ROS polynucleotide or truncated ROSpolynucleotide of the invention should be operatively linked to anappropriate promoter, such as the phage lambda PL promoter, the E. colilac, trp and tac promoters, the SV40 early and late promoters andpromoters of retroviral LTRs, to name a few. Other suitable promotersare known to the skilled artisan. The expression constructs will furthercontain sites for transcription initiation, termination and, in thetranscribed region, a ribosome binding site for translation. The codingportion of the mature transcripts expressed by the constructs willpreferably include a translation initiating at the beginning and atermination codon (UAA, UGA or UAG) appropriately positioned at the endof the polypeptide to be translated.

As indicated, the expression vectors will preferably include at leastone selectable marker. Such markers include dihydrofolate reductase orneomycin resistance for eukaryotic cell culture and tetracycline orampicillin resistance genes for culturing in E. coli and other bacteria.Representative examples of appropriate hosts include, but are notlimited to, bacterial cells, such as E. coli, Streptomyces andSalmonella typhimurium cells; fungal cells, such as yeast cells; insectcells such as Drosophila S2 and Spodoptera Sf9 cells; animal cells suchas CHO, COS and Bowes melanoma cells; and plant cells. Appropriateculture mediums and conditions for the above-described host cells areknown in the art.

Among vectors preferred for use in bacteria include pQE70, pQE60 andpQE-9, available from Qiagen; pBS vectors, Phagescript vectors,Bluescript vectors, pNH8A, pNH16a, pNH18A, pNH46A, available fromStratagene; and ptrc99a, pKK223-3, pKK233-3, pDR540, pRIT5 availablefrom Pharmacia. Among preferred eukaryotic vectors are pWLNEO, pSV2CAT,pOG44, pXT1 and pSG available from Stratagene; and pSVK3, pBPV, pMSG andpSVL available from Pharmacia. Other suitable vectors will be readilyapparent to the skilled artisan.

Among known bacterial promoters suitable for use in the presentinvention include the E. coli lacI and lacZ promoters, the T3 and T7promoters, the gpt promoter, the lambda PR and PL promoters and the trppromoter. Suitable eukaryotic promoters include the CMV immediate earlypromoter, the HSV thymidine kinase promoter, the early and late SV40promoters, the promoters of retroviral LTRs, such as those of the Roussarcoma virus (RSV), and metallothionein promoters, such as the mousemetallothionein-I promoter.

In the yeast, Saccharomyces cerevisiae, a number of vectors containingconstitutive or inducible promoters such as alpha factor, alcoholoxidase, and PGH may be used. For reviews, see Ausubel et al. (1989)CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, New York,N.Y., and Grant et al., Methods Enzymol. 153: 516-544 (1997).

Introduction of the construct into the host cell can be effected bycalcium phosphate transfection, DEAE-dextran mediated transfection,cationic lipid-mediated transfection, electroporation, transduction,infection or other methods. Such methods are described in many standardlaboratory manuals, such as Davis et al., BASIC METHODS IN MOLECULARBIOLOGY (1986).

Transcription of DNA encoding a CD74-ROS fusion polypeptide of thepresent invention by higher eukaryotes may be increased by inserting anenhancer sequence into the vector. Enhancers are cis-acting elements ofDNA, usually about from 10 to 300 bp that act to increasetranscriptional activity of a promoter in a given host cell-type.Examples of enhancers include the SV40 enhancer, which is located on thelate side of the replication origin at basepairs 100 to 270, thecytomegalovirus early promoter enhancer, the polyoma enhancer on thelate side of the replication origin, and adenovirus enhancers.

For secretion of the translated protein into the lumen of theendoplasmic reticulum, into the periplasmic space or into theextracellular environment, appropriate secretion signals may beincorporated into the expressed polypeptide. The signals may beendogenous to the polypeptide or they may be heterologous signals.

The polypeptide may be expressed in a modified form, such as a fusionprotein (e.g. a GST-fusion), and may include not only secretion signals,but also additional heterologous functional regions. For instance, aregion of additional amino acids, particularly charged amino acids, maybe added to the N-terminus of the polypeptide to improve stability andpersistence in the host cell, during purification, or during subsequenthandling and storage. Also, peptide moieties may be added to thepolypeptide to facilitate purification. Such regions may be removedprior to final preparation of the polypeptide. The addition of peptidemoieties to polypeptides to engender secretion or excretion, to improvestability and to facilitate purification, among others, are familiar androutine techniques in the art. A preferred fusion protein comprises aheterologous region from immunoglobulin that is useful to solubilizeproteins.

For example, EP-A-O 464 533 (Canadian counterpart 2045869) disclosesfusion proteins comprising various portions of constant region ofimmunoglobin molecules together with another human protein or partthereof. In many cases, the Fc part in a fusion protein is thoroughlyadvantageous for use in therapy and diagnosis and thus results, forexample, in improved pharmacokinetic properties (EP-A 0232 262). On theother hand, for some uses it would be desirable to be able to delete theFc part after the fusion protein has been expressed, detected andpurified in the advantageous manner described. This is the case when Fcportion proves to be a hindrance to use in therapy and diagnosis, forexample when the fusion protein is to be used as antigen forimmunizations. In drug discovery, for example, human proteins, such as,hIL5-has been fused with Fc portions for the purpose of high-throughputscreening assays to identify antagonists of hIL-5. See Bennett et al.,Journal of Molecular Recognition 8: 52-58 (1995) and Johanson et al.,The Journal of Biological Chemistry 270(16): 9459-9471 (1995).

CD74-ROS polypeptides can be recovered and purified from recombinantcell cultures by well-known methods including ammonium sulfate orethanol precipitation, acid extraction, anion or cation exchangechromatography, phosphocellulose chromatography, hydrophobic interactionchromatography, affinity chromatography, hydroxylapatite chromatographyand lectin chromatography. Most preferably, high performance liquidchromatography (“HPLC”) is employed for purification. Polypeptides ofthe present invention include naturally purified products, products ofchemical synthetic procedures, and products produced by recombinanttechniques from a prokaryotic or eukaryotic host, including, forexample, bacterial, yeast, higher plant, insect and mammalian cells.Depending upon the host employed in a recombinant production procedure,the polypeptides of the present invention may be glycosylated or may benon-glycosylated. In addition, polypeptides of the invention may alsoinclude an initial modified methionine residue, in some cases as aresult of host-mediated processes.

Accordingly, in one embodiment, the invention provides a method forproducing a recombinant CD74-ROS fusion polypeptide by culturing arecombinant host cell (as described above) under conditions suitable forthe expression of the fusion polypeptide and recovering the polypeptide.Culture conditions suitable for the growth of host cells and theexpression of recombinant polypeptides from such cells are well known tothose of skill in the art. See, e.g., CURRENT PROTOCOLS IN MOLECULARBIOLOGY, Ausubel F M et al., eds., Volume 2. Chapter 16, WileyInterscience.

D. Isolated Polypeptides.

The invention also provides, in part, isolated CD74-ROS fusionpolypeptides and fragments thereof. In one embodiment, the inventionprovides an isolated polypeptide comprising an amino acid sequence atleast 95% identical to a sequence selected from the group consisting of:(a) an amino acid sequence encoding a CD74-ROS fusion polypeptidecomprising the amino acid sequence of SEQ ID NO: 1; (b) an amino acidsequence encoding a CD74-ROS fusion polypeptide comprising theN-terminal amino acid sequence of CD74 (residues 1-208 of SEQ ID NO: 3)and the kinase domain of ROS (residues 1945-2222 of SEQ ID NO: 5); and(c) an amino acid sequence encoding a polypeptide comprising at leastsix contiguous amino acids encompassing the fusion junction (residues208-209 of SEQ ID NO: 1 or residues 208-209 of SEQ ID NO: 3) of aCD74-ROS fusion polypeptide; In one preferred embodiment, the inventionprovides an isolated CD74-ROS fusion polypeptide having the amino acidsequence encoded by the deposited cDNA described above. In anotherpreferred embodiment, recombinant mutant polypeptides of the inventionare provided, which may be produced using a recombinant vector orrecombinant host cell as described above.

It will be recognized in the art that some amino acid sequences of aCD74-ROS fusion polypeptide can be varied without significant effect ofthe structure or function of the mutant protein. If such differences insequence are contemplated, it should be remembered that there will becritical areas on the protein which determine activity (e.g. the kinasedomain of ROS). In general, it is possible to replace residues that formthe tertiary structure, provided that residues performing a similarfunction are used. In other instances, the type of residue may becompletely unimportant if the alteration occurs at a non-critical regionof the protein.

Thus, the invention further includes variations of a CD74-ROS fusionpolypeptide that show substantial ROS kinase activity or that includeregions of CD74 and ROS proteins, such as the protein portions discussedbelow. Such mutants include deletions, insertions, inversions, repeats,and type substitutions (for example, substituting one hydrophilicresidue for another, but not strongly hydrophilic for stronglyhydrophobic as a rule). Small changes or such “neutral” amino acidsubstitutions will generally have little effect on activity.

Typically seen as conservative substitutions are the replacements, onefor another, among the aliphatic amino acids Ala, Val, Leu and Ile;interchange of the hydroxyl residues Ser and Thr, exchange of the acidicresidues Asp and Glu, substitution between the amide residues Asn andGin, exchange of the basic residues Lys and Arg and replacements amongthe aromatic residues Phe, Tyr. Examples of conservative amino acidsubstitutions known to those skilled in the art are: Aromatic:phenylalanine tryptophan tyrosine; Hydrophobic: leucine isoleucinevaline; Polar: glutamine asparagines; Basic: arginine lysine histidine;Acidic: aspartic acid glutamic acid; Small: alanine serine threoninemethionine glycine. As indicated in detail above, further guidanceconcerning which amino acid changes are likely to be phenotypicallysilent (i.e., are not likely to have a significant deleterious effect ona function) can be found in Bowie et al., Science 247, supra.

The polypeptides of the present invention are preferably provided in anisolated form, and preferably are substantially purified. Arecombinantly produced version of a CD74-ROS fusion polypeptide of theinvention can be substantially purified by the one-step method describedin Smith and Johnson, Gene 67: 31-40 (1988).

The polypeptides of the present invention include the CD74-ROS fusionpolypeptides of FIG. 2 (SEQ ID NOs: 1) (whether or not including aleader sequence), the fusion polypeptide encoded by the deposited cDNAclone, an amino acid sequence encoding a CD74-ROS fusion polypeptidecomprising the N-terminal amino acid sequence of CD74 (residues 1-208 ofSEQ ID NO: 5) and the kinase domain of ROS (residues 1945-2222 of SEQ IDNO: 7), and an amino acid sequence encoding a polypeptide comprising atleast six contiguous amino acids encompassing the fusion junction(residues 208-209 of SEQ ID NO: 1) of a CD74-ROS fusion polypeptide, aswell as polypeptides that have at least 90% similarity, more preferablyat least 95% similarity, and still more preferably at least 96%, 97%,98% or 99% similarity to those described above.

By “% similarity” for two polypeptides is intended a similarity scoreproduced by comparing the amino acid sequences of the two polypeptidesusing the Bestfit program (Wisconsin Sequence Analysis Package. Version8 for Unix, Genetics Computer Group. University Research Park, 575Science Drive, Madison, Wis. 53711) and the default settings fordetermining similarity. Bestfit uses the local homology algorithm ofSmith and Waterman (Advances in Applied Mathematics 2: 482-489 (1981))to find the best segment of similarity between two sequences.

By a polypeptide having an amino acid sequence at least, for example,95% “identical” to a reference amino acid sequence of a mutant ROSpolypeptide of the invention is intended that the amino acid sequence ofthe polypeptide is identical to the reference sequence except that thepolypeptide sequence may include up to five amino acid alterations pereach 100 amino acids of the reference amino acid sequence of theCD74-ROS fusion polypeptide. In other words, to obtain a polypeptidehaving an amino acid sequence at least 95% identical to a referenceamino acid sequence, up to 5% of the amino acid residues in thereference sequence may be deleted or substituted with another aminoacid, or a number of amino acids up to 5% of the total amino acidresidues in the reference sequence may be inserted into the referencesequence. These alterations of the reference sequence may occur at theamino or carboxy terminal positions of the reference amino acid sequenceor anywhere between those terminal positions, interspersed eitherindividually among residues in the reference sequence or in one or morecontiguous groups within the reference sequence.

When using Bestfit or any other sequence alignment program to determinewhether a particular sequence is, for instance, 95% identical to areference sequence according to the present invention, the parametersare set, of course, such that the percentage of identity is calculatedover the full length of the reference amino acid sequence and that gapsin homology of up to 5% of the total number of amino acid residues inthe reference sequence are allowed.

A CD74-ROS fusion polypeptide of the present invention could be used asa molecular weight marker on SDS-PAGE gels or on molecular sieve gelfiltration columns, for example, using methods well known to those ofskill in the art.

As further described in detail below, the polypeptides of the presentinvention can also be used to generate fusion polypeptide specificreagents, such as polyclonal and monoclonal antibodies, which are usefulin assays for detecting mutant ROS polypeptide expression as describedbelow or as agonists and antagonists capable of enhancing or inhibitingmutant ROS protein function/activity. Further, such polypeptides can beused in the yeast two-hybrid system to “capture” CD74-ROS fusionpolypeptide binding proteins, which are also candidate agonist andantagonist according to the present invention. The yeast two hybridsystem is described in Fields and Song, Nature 340: 245-246 (1989).

In another aspect, the invention provides a peptide or polypeptidecomprising an epitope-bearing portion of a polypeptide of the invention,namely an epitope comprising the fusion junction of a CD74-ROS fusionpolypeptide variant The epitope of this polypeptide portion is animmunogenic or antigenic epitope of a polypeptide of the invention. An“immunogenic epitope” is defined as a part of a protein that elicits anantibody response when the whole protein is the immunogen. Theseimmunogenic epitopes are believed to be confined to a few loci on themolecule. On the other hand, a region of a protein molecule to which anantibody can bind is defined as an “antigenic epitope.” The number ofimmunogenic epitopes of a protein generally is less than the number ofantigenic epitopes. See, for instance, Geysen et al., Proc. Natl. Acad.Sci. USA 81:3998-4002 (1983). The production of fusionpolypeptide-specific antibodies of the invention is described in furtherdetail below.

The antibodies raised by antigenic epitope-bearing peptides orpolypeptides are useful to detect a mimicked protein, and antibodies todifferent peptides may be used for tracking the fate of various regionsof a protein precursor which undergoes post-translational processing.The peptides and anti-peptide antibodies may be used in a variety ofqualitative or quantitative assays for the mimicked protein, forinstance in competition assays since it has been shown that even shortpeptides (e.g., about 9 amino acids) can bind and displace the largerpeptides in immunoprecipitation assays. See, for instance, Wilson etal., Cell 37: 767-778 (1984) at 777. The anti-peptide antibodies of theinvention also are useful for purification of the mimicked protein, forinstance, by adsorption chromatography using methods well known in theart. Immunological assay formats are described in further detail below.

Recombinant mutant ROS kinase polypeptides are also within the scope ofthe present invention, and may be producing using fusion polynucleotidesof the invention, as described in Section B above. For example, theinvention provides a method for producing a recombinant CD74-ROS fusionpolypeptide by culturing a recombinant host cell (as described above)under conditions suitable for the expression of the fusion polypeptideand recovering the polypeptide. Culture conditions suitable for thegrowth of host cells and the expression of recombinant polypeptides fromsuch cells are well known to those of skill in the art.

E. Mutant-Specific Reagents

Mutant ROS polypeptide-specific reagents useful in the practice of thedisclosed methods include, among others, fusion polypeptide specificantibodies and AQUA peptides (heavy-isotope labeled peptides)corresponding to, and suitable for detection and quantification of,CD74-ROS fusion polypeptide expression in a biological sample. A fusionpolypeptide-specific reagent is any reagent, biological or chemical,capable of specifically binding to, detecting and/or quantifying thepresence/level of expressed CD74-ROS fusion polypeptide in a biologicalsample. The term includes, but is not limited to, the preferred antibodyand AQUA peptide reagents discussed below, and equivalent reagents arewithin the scope of the present invention.

Antibodies.

Reagents suitable for use in practice of the methods of the inventioninclude a CD74-ROS fusion polypeptide-specific antibody. Afusion-specific antibody of the invention is an isolated antibody orantibodies that specifically bind(s) a CD74-ROS fusion polypeptide ofthe invention (e.g. SEQ ID NO: 1) but does not substantially bind eitherwild type CD74 or wild type ROS. Other suitable reagents includeepitope-specific antibodies that specifically bind to an epitope in theextracellular domain of wild type ROS protein sequence (which domain isnot present in the truncated ROS kinase disclosed herein), and aretherefore capable of detecting the presence (or absence) of wild typeROS in a sample.

Human CD74-ROS fusion polypeptide-specific antibodies may also bind tohighly homologous and equivalent epitopic peptide sequences in othermammalian species, for example murine or rabbit, and vice versa.Antibodies useful in practicing the methods of the invention include (a)monoclonal antibodies. (b) purified polyclonal antibodies thatspecifically bind to the target polypeptide (e.g. the fusion junction ofCD74-ROS fusion polypeptide, (c) antibodies as described in (a)-(b)above that bind equivalent and highly homologous epitopes orphosphorylation sites in other non-human species (e.g. mouse, rat), and(d) fragments of (a)-(c) above that bind to the antigen (or morepreferably the epitope) bound by the exemplary antibodies disclosedherein.

The term “antibody” or “antibodies” as used herein refers to all typesof immunoglobulins, including IgG, IgM, IgA, IgD, and IgE. Theantibodies may be monoclonal or polyclonal and may be of any species oforigin, including (for example) mouse, rat, rabbit, horse, or human, ormay be chimeric antibodies. See, e.g., M. Walker et al., Molec. Immunol.26: 403-11 (1989); Morrision et al., Proc. Nat'l. Acad. Sci. 81: 6851(1984); Neuberger et al., Nature 312: 604 (1984)). The antibodies may berecombinant monoclonal antibodies produced according to the methodsdisclosed in U.S. Pat. No. 4,474,893 (Reading) or U.S. Pat. No.4,816,567 (Cabilly et al.) The antibodies may also be chemicallyconstructed specific antibodies made according to the method disclosedin U.S. Pat. No. 4,676,980 (Segel et al.) The preferred epitopic site ofa CD74-ROS fusion polypeptide specific antibody of the invention is apeptide fragment consisting essentially of about 11 to 17 amino acids ofa human CD74-ROS fusion polypeptide sequence (SEQ ID NOs: 1) whichfragment encompasses the fusion junction (which occurs at residue 208 inthe first and second fusion protein variants (see FIG. 1 (panel C) andFIG. 7 (bottom panel)). It will be appreciated that antibodies thatspecifically binding shorter or longer peptides/epitopes encompassingthe fusion junction of a CD74-ROS fusion polypeptide are within thescope of the present invention.

The invention is not limited to use of antibodies, but includesequivalent molecules, such as protein binding domains or nucleic acidaptamers, which bind, in a fusion-protein or truncated-protein specificmanner, to essentially the same epitope to which a CD74-ROS fusionpolypeptide-specific antibody or ROS truncation point epitope-specificantibody useful in the methods of the invention binds. See, e.g.,Neuberger et al., Nature 312: 604 (1984). Such equivalent non-antibodyreagents may be suitably employed in the methods of the inventionfurther described below.

Polyclonal antibodies useful in practicing the methods of the inventionmay be produced according to standard techniques by immunizing asuitable animal (e.g., rabbit, goat, etc.) with an antigen encompassinga desired fusion-protein specific epitope (e.g. the fusion junction,collecting immune serum from the animal, and separating the polyclonalantibodies from the immune serum, and purifying polyclonal antibodieshaving the desired specificity, in accordance with known procedures. Theantigen may be a synthetic peptide antigen comprising the desiredepitopic sequence, selected and constructed in accordance withwell-known techniques. See. e.g., ANTIBODIES: A LABORATORY MANUAL,Chapter 5, p. 75-76, Harlow & Lane Eds., Cold Spring Harbor Laboratory(1988); Czernik, Methods In Enzymology, 201: 264-283 (1991); Merrifield,J. Am. Chem. Soc. 85: 21-49 (1962)). Polyclonal antibodies produced asdescribed herein may be screened and isolated as further describedbelow.

Monoclonal antibodies may also be beneficially employed in the methodsof the invention, and may be produced in hybridoma cell lines accordingto the well-known technique of Kohler and Milstein. Nature 265: 495-97(1975); Kohler and Milstein, Eur. J. Immunol. 6: 511 (1976); see also,CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, Ausubel et al. Eds. (1989).Monoclonal antibodies so produced are highly specific, and improve theselectivity and specificity of assay methods provided by the invention.For example, a solution containing the appropriate antigen (e.g. asynthetic peptide comprising the fusion junction of CD74-ROS fusionpolypeptide) may be injected into a mouse and, after a sufficient time(in keeping with conventional techniques), the mouse sacrificed andspleen cells obtained. The spleen cells are then immortalized by fusingthem with myeloma cells, typically in the presence of polyethyleneglycol, to produce hybridoma cells. Rabbit fusion hybridomas, forexample, may be produced as described in U.S. Pat. No. 5,675,063, C.Knight, Issued Oct. 7, 1997. The hybridoma cells are then grown in asuitable selection media, such as hypoxanthine-aminopterin-thymidine(HAT), and the supernatant screened for monoclonal antibodies having thedesired specificity, as described below. The secreted antibody may berecovered from tissue culture supernatant by conventional methods suchas precipitation, ion exchange or affinity chromatography, or the like.

Monoclonal Fab fragments may also be produced in Escherichia coli byrecombinant techniques known to those skilled in the art. See, e.g., W.Huse, Science 246: 1275-81 (1989); Mullinax et al., Proc. Nat'l Acad.Sci. 87: 8095 (1990). If monoclonal antibodies of one isotype arepreferred for a particular application, particular isotypes can beprepared directly, by selecting from the initial fusion, or preparedsecondarily, from a parental hybridoma secreting a monoclonal antibodyof different isotype by using the sib selection technique to isolateclass-switch variants (Steplewski, et al., Proc. Nat'l. Acad. Sci., 82:8653 (1985); Spira et al., J. Immunol. Methods 74: 307 (1984)). Theantigen combining site of the monoclonal antibody can be cloned by PCRand single-chain antibodies produced as phage-displayed recombinantantibodies or soluble antibodies in E. coli (see, e.g., ANTIBODYENGINEERING PROTOCOLS, 1995, Humana Press, Sudhir Paul editor.)

Further still, U.S. Pat. No. 5,194,392, Geysen (1990) describes ageneral method of detecting or determining the sequence of monomers(amino acids or other compounds) which is a topological equivalent ofthe epitope (i.e., a “mimotope”) which is complementary to a particularparatope (antigen binding site) of an antibody of interest. Moregenerally, this method involves detecting or determining a sequence ofmonomers which is a topographical equivalent of a ligand which iscomplementary to the ligand binding site of a particular receptor ofinterest. Similarly, U.S. Pat. No. 5,480,971, Houghten et al. (1996)discloses linear C₁-C-alkyl peralkylated oligopeptides and sets andlibraries of such peptides, as well as methods for using sucholigopeptide sets and libraries for determining the sequence of aperalkylated oligopeptide that preferentially binds to an acceptormolecule of interest. Thus, non-peptide analogs of the epitope-bearingpeptides of the invention also can be made routinely by these methods.

Antibodies useful in the methods of the invention, whether polyclonal ormonoclonal, may be screened for epitope and fusion protein specificityaccording to standard techniques. See, e.g. Czernik et al., Methods inEnzymology, 201: 264-283 (1991). For example, the antibodies may bescreened against a peptide library by ELISA to ensure specificity forboth the desired antigen and, if desired, for reactivity only with aCD74-ROS fusion polypeptide of the invention and not with wild type CD74or wild type ROS. The antibodies may also be tested by Western blottingagainst cell preparations containing target protein to confirmreactivity with the only the desired target and to ensure no appreciablebinding to other fusion proteins involving ROS. The production,screening, and use of fusion protein-specific antibodies is known tothose of skill in the art, and has been described. See, e.g., U.S.Patent Publication No. 20050214301, Wetzel et al., Sep. 29, 2005.

Fusion polypeptide-specific antibodies useful in the methods of theinvention may exhibit some limited cross-reactivity with similar fusionepitopes in other fusion proteins or with the epitopes in wild type CD74and wild type ROS that form the fusion junction. This is not unexpectedas most antibodies exhibit some degree of cross-reactivity, andanti-peptide antibodies will often cross-react with epitopes having highhomology or identity to the immunizing peptide. See, e.g., Czernik,supra. Cross-reactivity with other fusion proteins is readilycharacterized by Western blotting alongside markers of known molecularweight. Amino acid sequences of cross-reacting proteins may be examinedto identify sites highly homologous or identical to the CD74-ROS fusionpolypeptide sequence to which the antibody binds. Undesirablecross-reactivity can be removed by negative selection using antibodypurification on peptide columns (e.g. selecting out antibodies that bindeither wild type CD74 and/or wild type ROS).

CD74-ROS fusion polypeptide-specific antibodies of the invention thatare useful in practicing the methods disclosed herein are ideallyspecific for human fusion polypeptide, but are not limited only tobinding the human species, per se. The invention includes the productionand use of antibodies that also bind conserved and highly homologous oridentical epitopes in other mammalian species (e.g. mouse, rat, monkey).Highly homologous or identical sequences in other species can readily beidentified by standard sequence comparisons, such as using BLAST, withthe human CD74-ROS fusion polypeptide sequences disclosed herein (SEQ IDNOs: 1).

Antibodies employed in the methods of the invention may be furthercharacterized by, and validated for, use in a particular assay format,for example FC, IHC, and/or ICC. The use of CD74-ROS fusionpolypeptide-specific antibodies in such methods is further described inSection F below. Antibodies may also be advantageously conjugated tofluorescent dyes (e.g. Alexa488, PE), or labels such as quantum dots,for use in multi-parametric analyses along with other signaltransduction (phospho-AKT, phospho-Erk ½) and/or cell marker(cytokeratin) antibodies, as further described in Section F below.

In practicing the methods of the invention, the expression and/oractivity of wild type CD74 and/or wild type ROS in a given biologicalsample may also be advantageously examined using antibodies (eitherphospho-specific or total) for these wild type proteins. For example,CSF receptor phosphorylation-site specific antibodies are commerciallyavailable (see CELL SIGNALING TECHNOLOGY, INC., Beverly Mass., 2005/06Catalogue, #'s 3151, 3155, and 3154; and Upstate Biotechnology, 2006Catalogue, #06-457). Such antibodies may also be produced according tostandard methods, as described above. The amino acid sequences of bothhuman CD74 and ROS are published (see FIGS. 3 and 4, and referencedSwissProt Accession Nos.), as are the sequences of these proteins fromother species.

Detection of wild type CD74 and wild type ROS expression and/oractivation, along with CD74-ROS fusion polypeptide expression, in abiological sample (e.g. a tumor sample) can provide information onwhether the fusion protein alone is driving the tumor, or whether wildtype ROS is also activated and driving the tumor. Such information isclinically useful in assessing whether targeting the fusion protein orthe wild type protein(s), or both, or is likely to be most beneficial ininhibiting progression of the tumor, and in selecting an appropriatetherapeutic or combination thereof. Antibodies specific for the wildtype ROS kinase extracellular domain, which is not present in thetruncated ROS kinase disclosed herein, may be particularly useful fordetermining the presence/absence of the mutant ROS kinase.

It will be understood that more than one antibody may be used in thepractice of the above-described methods. For example, one or moreCD74-ROS fusion polypeptide-specific antibodies together with one ormore antibodies specific for another kinase, receptor, or kinasesubstrate that is suspected of being, or potentially is, activated in acancer in which CD74-ROS fusion polypeptide is expressed may besimultaneously employed to detect the activity of such other signalingmolecules in a biological sample comprising cells from such cancer.

Those of skill in the art will appreciate that CD74-ROS fusionpolypeptides of the present invention and the fusion junctionepitope-bearing fragments thereof described above can be combined withparts of the constant domain of immunoglobulins (IgG), resulting inchimeric polypeptides. These fusion proteins facilitate purification andshow an increased half-life in vivo. This has been shown, e.g., forchimeric proteins consisting of the first two domains of the humanCD4-polypeptide and various domains of the constant regions of the heavyor light chains of mammalian immunoglobulins (EPA 394.827; Traunecker etal., Nature 331: 84-86 (1988)). Fusion proteins that have adisulfide-linked dimeric structure due to the IgG part can also be moreefficient in binding and neutralizing other molecules than the monomericCD74-ROS fusion polypeptide alone (Fountoulakis et al., J. Biochem 270:3958-3964 (1995)).

Heavy-Isotope Labeled Peptides (AQUA Peptides).

CD74-ROS fusion polypeptide-specific reagents useful in the practice ofthe disclosed methods may also comprise heavy-isotope labeled peptidessuitable for the absolute quantification of expressed CD74-ROS fusionpolypeptide in a biological sample. The production and use of AQUApeptides for the absolute quantification of proteins (AQUA) in complexmixtures has been described. See WO/03016861, “Absolute Quantificationof Proteins and Modified Forms Thereof by Multistage Mass Spectrometry,”Gygi et al, and also Gerber et al. Proc. Natl. Acad. Sci. U.S.A. 100:6940-5 (2003) (the teachings of which are hereby incorporated herein byreference, in their entirety).

The AQUA methodology employs the introduction of a known quantity of atleast one heavy-isotope labeled peptide standard (which has a uniquesignature detectable by LC-SRM chromatography) into a digestedbiological sample in order to determine, by comparison to the peptidestandard, the absolute quantity of a peptide with the same sequence andprotein modification in the biological sample. Briefly, the AQUAmethodology has two stages: peptide internal standard selection andvalidation and method development; and implementation using validatedpeptide internal standards to detect and quantify a target protein insample. The method is a powerful technique for detecting and quantifyinga given peptide/protein within a complex biological mixture, such as acell lysate, and may be employed. e.g., to quantify change in proteinphosphorylation as a result of drug treatment, or to quantifydifferences in the level of a protein in different biological states.

Generally, to develop a suitable internal standard, a particular peptide(or modified peptide) within a target protein sequence is chosen basedon its amino acid sequence and the particular protease to be used todigest. The peptide is then generated by solid-phase peptide synthesissuch that one residue is replaced with that same residue containingstable isotopes (¹³C, ¹⁵N). The result is a peptide that is chemicallyidentical to its native counterpart formed by proteolysis, but is easilydistinguishable by MS via a 7-Da mass shift. The newly synthesized AQUAinternal standard peptide is then evaluated by LC-MS/MS. This processprovides qualitative information about peptide retention byreverse-phase chromatography, ionization efficiency, and fragmentationvia collision-induced dissociation. Informative and abundant fragmentions for sets of native and internal standard peptides are chosen andthen specifically monitored in rapid succession as a function ofchromatographic retention to form a selected reaction monitoring(LC-SRM) method based on the unique profile of the peptide standard.

The second stage of the AQUA strategy is its implementation to measurethe amount of a protein or modified protein from complex mixtures. Wholecell lysates are typically fractionated by SDS-PAGE gel electrophoresis,and regions of the gel consistent with protein migration are excised.This process is followed by in-gel proteolysis in the presence of theAQUA peptides and LC-SRM analysis. (See Gerber et al. supra.) AQUApeptides are spiked in to the complex peptide mixture obtained bydigestion of the whole cell lysate with a proteolytic enzyme andsubjected to immunoaffinity purification as described above. Theretention time and fragmentation pattern of the native peptide formed bydigestion (e.g. trypsinization) is identical to that of the AQUAinternal standard peptide determined previously, thus, LC-MS/MS analysisusing an SRM experiment results in the highly specific and sensitivemeasurement of both internal standard and analyte directly fromextremely complex peptide mixtures.

Since an absolute amount of the AQUA peptide is added (e.g. 250 fmol),the ratio of the areas under the curve can be used to determine theprecise expression levels of a protein or phosphorylated form of aprotein in the original cell lysate. In addition, the internal standardis present during in-gel digestion as native peptides are formed, suchthat peptide extraction efficiency from gel pieces, absolute lossesduring sample handling (including vacuum centrifugation), andvariability during introduction into the LC-MS system do not affect thedetermined ratio of native and AQUA peptide abundances.

An AQUA peptide standard is developed for a known sequence previouslyidentified by the IAP-LC-MS/MS method within in a target protein. If thesite is modified, one AQUA peptide incorporating the modified form ofthe particular residue within the site may be developed, and a secondAQUA peptide incorporating the unmodified form of the residue developed.In this way, the two standards may be used to detect and quantify boththe modified an unmodified forms of the site in a biological sample.

Peptide internal standards may also be generated by examining theprimary amino acid sequence of a protein and determining the boundariesof peptides produced by protease cleavage. Alternatively, a protein mayactually be digested with a protease and a particular peptide fragmentproduced can then sequenced. Suitable proteases include, but are notlimited to, serine proteases (e.g. trypsin, hepsin), metallo proteases(e.g. PUMP1), chymotrypsin, cathepsin, pepsin, thermolysin,carboxypeptidases, etc.

A peptide sequence within a target protein is selected according to oneor more criteria to optimize the use of the peptide as an internalstandard. Preferably, the size of the peptide is selected to minimizethe chances that the peptide sequence will be repeated elsewhere inother non-target proteins. Thus, a peptide is preferably at least about6 amino acids. The size of the peptide is also optimized to maximizeionization frequency. Thus, peptides longer than about 20 amino acidsare not preferred. The preferred ranged is about 7 to 15 amino acids. Apeptide sequence is also selected that is not likely to be chemicallyreactive during mass spectrometry, thus sequences comprising cysteine,tryptophan, or methionine are avoided.

A peptide sequence that does not include a modified region of the targetregion may be selected so that the peptide internal standard can be usedto determine the quantity of all forms of the protein. Alternatively, apeptide internal standard encompassing a modified amino acid may bedesirable to detect and quantify only the modified form of the targetprotein. Peptide standards for both modified and unmodified regions canbe used together, to determine the extent of a modification in aparticular sample (i.e. to determine what fraction of the total amountof protein is represented by the modified form). For example, peptidestandards for both the phosphorylated and unphosphorylated form of aprotein known to be phosphorylated at a particular site can be used toquantify the amount of phosphorylated form in a sample.

The peptide is labeled using one or more labeled amino acids (i.e. thelabel is an actual part of the peptide) or less preferably, labels maybe attached after synthesis according to standard methods. Preferably,the label is a mass-altering label selected based on the followingconsiderations: The mass should be unique to shift fragments massesproduced by MS analysis to regions of the spectrum with low background;the ion mass signature component is the portion of the labeling moietythat preferably exhibits a unique ion mass signature in MS analysis; thesum of the masses of the constituent atoms of the label is preferablyuniquely different than the fragments of all the possible amino acids.As a result, the labeled amino acids and peptides are readilydistinguished from unlabeled ones by the ion/mass pattern in theresulting mass spectrum. Preferably, the ion mass signature componentimparts a mass to a protein fragment that does not match the residuemass for any of the 20 natural amino acids.

The label should be robust under the fragmentation conditions of MS andnot undergo unfavorable fragmentation. Labeling chemistry should beefficient under a range of conditions, particularly denaturingconditions, and the labeled tag preferably remains soluble in the MSbuffer system of choice. The label preferably does not suppress theionization efficiency of the protein and is not chemically reactive. Thelabel may contain a mixture of two or more isotopically distinct speciesto generate a unique mass spectrometric pattern at each labeled fragmentposition. Stable isotopes, such as ²H, ¹³C, ¹⁵N, ¹⁷O, ¹⁸O, or ³⁴S, areamong preferred labels. Pairs of peptide internal standards thatincorporate a different isotope label may also be prepared. Preferredamino acid residues into which a heavy isotope label may be incorporatedinclude leucine, proline, valine, and phenylalanine.

Peptide internal standards are characterized according to theirmass-to-charge (m/z) ratio, and preferably, also according to theirretention time on a chromatographic column (e.g. an HPLC column).Internal standards that co-elute with unlabeled peptides of identicalsequence are selected as optimal internal standards. The internalstandard is then analyzed by fragmenting the peptide by any suitablemeans, for example by collision-induced dissociation (CID) using, e.g.,argon or helium as a collision gas. The fragments are then analyzed, forexample by multi-stage mass spectrometry (MS^(n)) to obtain a fragmention spectrum, to obtain a peptide fragmentation signature. Preferably,peptide fragments have significant differences in m/z ratios to enablepeaks corresponding to each fragment to be well separated, and asignature is that is unique for the target peptide is obtained. If asuitable fragment signature is not obtained at the first stage,additional stages of MS are performed until a unique signature isobtained.

Fragment ions in the MS/MS and MS³ spectra are typically highly specificfor the peptide of interest, and, in conjunction with LC methods, allowa highly selective means of detecting and quantifying a targetpeptide/protein in a complex protein mixture, such as a cell lysate,containing many thousands or tens of thousands of proteins. Anybiological sample potentially containing a target protein/peptide ofinterest may be assayed. Crude or partially purified cell extracts arepreferably employed. Generally, the sample has at least 0.01 mg ofprotein, typically a concentration of 0.1-10 mg/mL, and may be adjustedto a desired buffer concentration and pH.

A known amount of a labeled peptide internal standard, preferably about10 femtomoles, corresponding to a target protein to bedetected/quantified is then added to a biological sample, such as a celllysate. The spiked sample is then digested with one or more protease(s)for a suitable time period to allow digestion. A separation is thenperformed (e.g. by HPLC, reverse-phase HPLC, capillary electrophoresis,ion exchange chromatography, etc.) to isolate the labeled internalstandard and its corresponding target peptide from other peptides in thesample. Microcapillary LC is a preferred method.

Each isolated peptide is then examined by monitoring of a selectedreaction in the MS. This involves using the prior knowledge gained bythe characterization of the peptide internal standard and then requiringthe MS to continuously monitor a specific ion in the MS/MS or MS^(n)spectrum for both the peptide of interest and the internal standard.After elution, the area under the curve (AUC) for both peptide standardand target peptide peaks are calculated. The ratio of the two areasprovides the absolute quantification that can be normalized for thenumber of cells used in the analysis and the protein's molecular weightto provide the precise number of copies of the protein per cell. Furtherdetails of the AQUA methodology are described in Gygi et al., and Gerberet al. supra.

AQUA internal peptide standards (heavy-isotope labeled peptides) maydesirably be produced, as described above, to detect any quantify anyunique site (e.g. the fusion junction within a CD74-ROS fusionpolypeptide) within a mutant ROS polypeptide of the invention. Forexample, an AQUA phosphopeptide may be prepared that corresponds to thefusion junction sequence of CD74-ROS fusion polypeptide Peptidestandards for may be produced for the CD74-ROS fusion junction and suchstandards employed in the AQUA methodology to detect and quantify thefusion junction (i.e. the presence of CD74-ROS fusion polypeptide) in abiological sample.

For example, an exemplary AQUA peptide of the invention comprises theamino acid sequence LVGDDF, which corresponds to the three amino acidsimmediately flanking each side of the fusion junction in the second(short) variant of CD74-ROS fusion polypeptide. It will be appreciatedthat larger AQUA peptides comprising the fusion junction sequence (andadditional residues downstream or upstream of it) may also beconstructed. Similarly, a smaller AQUA peptide comprising less than allof the residues of such sequence (but still comprising the point offusion junction itself) may alternatively be constructed. Such larger orshorter AQUA peptides are within the scope of the present invention, andthe selection and production of preferred AQUA peptides may be carriedout as described above (see Gygi et al., Gerber et al., supra.).

Nucleic Acid Probes.

Fusion-specific reagents provided by the invention also include nucleicacid probes and primers suitable for detection of a CD74-ROSpolynucleotide, as described in detail in Section B above. The specificuse of such probes in assays such as fluorescence in-situ hybridization(FISH) or PCR amplification is described in Section F below.

Also provided by the invention is a kit for the detection of a CD74-ROSfusion polynucleotide and/or polypeptide in a biological sample, the kitcomprising at least one fusion polynucleotide- or polypeptide-specificreagent of the invention, and one or more secondary reagents. Suitablesecondary reagents for employment in a kit are familiar to those ofskill in the art, and include, by way of example, buffers, detectablesecondary antibodies or probes, kinases, activating agents, kinasesubstrates, and the like.

F. Diagnostic Applications & Assay Formats.

The methods of the invention may be carried out in a variety ofdifferent assay formats known to those of skill in the art.

Immunoassays.

Immunoassays useful in the practice of the methods of the invention maybe homogenous immunoassays or heterogeneous immunoassays. In ahomogeneous assay the immunological reaction usually involves a mutantROS polypeptide-specific reagent (e.g. a CD74-ROS fusionpolypeptide-specific antibody), a labeled analyte, and the biologicalsample of interest. The signal arising from the label is modified,directly or indirectly, upon the binding of the antibody to the labeledanalyte. Both the immunological reaction and detection of the extentthereof are carried out in a homogeneous solution. Immunochemical labelsthat may be employed include free radicals, radio-isotopes, fluorescentdyes, enzymes, bacteriophages, coenzymes, and so forth. Semi-conductornanocrystal labels, or “quantum dots”, may also be advantageouslyemployed, and their preparation and use has been well described. Seegenerally, K. Barovsky, Nanotech. Law & Bus. 1(2): Article 14 (2004) andpatents cited therein.

In a heterogeneous assay approach, the reagents are usually thebiological sample, a mutant ROS kinase polypeptide-specific reagent(e.g., an antibody), and suitable means for producing a detectablesignal. Biological samples as further described below may be used. Theantibody is generally immobilized on a support, such as a bead, plate orslide, and contacted with the sample suspected of containing the antigenin a liquid phase. The support is then separated from the liquid phaseand either the support phase or the liquid phase is examined for adetectable signal employing means for producing such signal. The signalis related to the presence of the analyte in the biological sample.Means for producing a detectable signal include the use of radioactivelabels, fluorescent labels, enzyme labels, quantum dots, and so forth.For example, if the antigen to be detected contains a second bindingsite, an antibody which binds to that site can be conjugated to adetectable group and added to the liquid phase reaction solution beforethe separation step. The presence of the detectable group on the solidsupport indicates the presence of the antigen in the test sample.Examples of suitable immunoassays are the radioimmunoassay,immunofluorescence methods, enzyme-linked immunoassays, and the like.

Immunoassay formats and variations thereof, which may be useful forcarrying out the methods disclosed herein, are well known in the art.See generally E. Maggio, Enzyme-Immunoassay, (1980) (CRC Press, Inc.,Boca Raton, Fla.); see also, e.g., U.S. Pat. No. 4,727,022 (Skold etal., “Methods for Modulating Ligand-Receptor Interactions and theirApplication”); U.S. Pat. No. 4,659,678 (Forrest et al., “Immunoassay ofAntigens”); U.S. Pat. No. 4,376,110 (David et al., “Immunometric AssaysUsing Monoclonal Antibodies”). Conditions suitable for the formation ofreagent-antibody complexes are well known to those of skill in the art.See id CD74-ROS fusion polypeptide-specific monoclonal antibodies may beused in a “two-site” or “sandwich” assay, with a single hybridoma cellline serving as a source for both the labeled monoclonal antibody andthe bound monoclonal antibody. Such assays are described in U.S. Pat.No. 4,376,110. The concentration of detectable reagent should besufficient such that the binding of CD74-ROS fusion polypeptide isdetectable compared to background.

Antibodies useful in the practice of the methods disclosed herein may beconjugated to a solid support suitable for a diagnostic assay (e.g.,beads, plates, slides or wells formed from materials such as latex orpolystyrene) in accordance with known techniques, such as precipitation.Antibodies or other CD74-ROS fusion polypeptide-binding reagents maylikewise be conjugated to detectable groups such as radiolabels (e.g.,³⁵S, ¹²⁵I, ¹³¹I), enzyme labels (e.g., horseradish peroxidase, alkalinephosphatase), and fluorescent labels (e.g., fluorescein) in accordancewith known techniques.

Cell-based assays, such flow cytometry (FC), immuno-histochemistry(IHC), or immunofluorescence (IF) are particularly desirable inpracticing the methods of the invention, since such assay formats areclinically-suitable, allow the detection of mutant ROS polypeptideexpression in vivo, and avoid the risk of artifact changes in activityresulting from manipulating cells obtained from, e.g. a tumor sample inorder to obtain extracts. Accordingly, in some preferred embodiment, themethods of the invention are implemented in a flow-cytometry (FC),immuno-histochemistry (IHC), or immunofluorescence (IF) assay format.

Flow cytometry (FC) may be employed to determine the expression ofmutant ROS polypeptide in a mammalian tumor before, during, and aftertreatment with a drug targeted at inhibiting ROS kinase activity. Forexample, tumor cells from a fine needle aspirate may be analyzed by flowcytometry for CD74-ROS fusion polypeptide expression and/or activation,as well as for markers identifying cancer cell types, etc., if sodesired. Flow cytometry may be carried out according to standardmethods. See, e.g. Chow et al., Cytometry (Communications in ClinicalCytometry) 46: 72-78 (2001). Briefly and by way of example, thefollowing protocol for cytometric analysis may be employed: fixation ofthe cells with 2% paraformaldehyde for 10 minutes at 37° C. followed bypermeabilization in 90% methanol f0 minutes on ice. Cells may then bestained with the primary CD74-ROS fusion polypeptide-specific antibody,washed and labeled with a fluorescent-labeled secondary antibody. Thecells would then be analyzed on a flow cytometer (e.g. a Beckman CoulterFC500) according to the specific protocols of the instrument used. Suchan analysis would identify the level of expressed CD74-ROS fusionpolypeptide in the tumor. Similar analysis after treatment of the tumorwith a ROS-inhibiting therapeutic would reveal the responsiveness of aCD74-ROS fusion polypeptide-expressing tumor to the targeted inhibitorof ROS kinase.

Immunohistochemical (IHC) staining may be also employed to determine theexpression and/or activation status of mutant ROS kinase polypeptide ina mammalian cancer (e.g. NSCLC) before, during, and after treatment witha drug targeted at inhibiting ROS kinase activity. IHC may be carriedout according to well-known techniques. See, e.g., ANTIBODIES: ALABORATORY MANUAL, Chapter 10, Harlow & Lane Eds., Cold Spring HarborLaboratory (1988). Briefly, and by way of example, paraffin-embeddedtissue (e.g. tumor tissue from a biopsy) is prepared forimmunohistochemical staining by deparaffinizing tissue sections withxylene followed by ethanol: hydrating in water then PBS: unmaskingantigen by heating slide in sodium citrate buffer; incubating sectionsin hydrogen peroxide; blocking in blocking solution; incubating slide inprimary anti-CD74-ROS fusion polypeptide antibody and secondaryantibody; and finally detecting using ABC avidin/biotin method accordingto manufacturer's instructions.

Immunofluorescence (IF) assays may be also employed to determine theexpression and/or activation status of CD74-ROS fusion polypeptide in amammalian cancer before, during, and after treatment with a drugtargeted at inhibiting ROS kinase activity. IF may be carried outaccording to well-known techniques. See, e.g., J. M. polak and S. VanNoorden (1997) INTRODUCTION TO IMMUNOCYTOCHEMISTRY, 2nd Ed.; ROYALMICROSCOPY SOCIETY MICROSCOPY HANDBOOK 37,BioScientific/Springer-Verlag. Briefly, and by way of example, patientsamples may be fixed in paraformaldehyde followed by methanol, blockedwith a blocking solution such as horse serum, incubated with the primaryantibody against CD74-ROS fusion polypeptide followed by a secondaryantibody labeled with a fluorescent dye such as Alexa 488 and analyzedwith an epifluorescent microscope.

Antibodies employed in the above-described assays may be advantageouslyconjugated to fluorescent dyes (e.g. Alexa488, PE), or other labels,such as quantum dots, for use in multi-parametric analyses along withother signal transduction (EGFR, phospho-AKT, phospho-Erk ½) and/or cellmarker (cytokeratin) antibodies.

A variety of other protocols, including enzyme-linked immunosorbentassay (ELISA), radio-immunoassay (RIA), and fluorescent-activated cellsorting (FACS), for measuring mutant ROS kinase polypeptides are knownin the art and provide a basis for diagnosing altered or abnormal levelsof CD74-ROS fusion polypeptide expression. Normal or standard values forCD74-ROS fusion polypeptide expression are established by combining bodyfluids or cell extracts taken from normal mammalian subjects, preferablyhuman, with antibody to CD74-ROS fusion polypeptide under conditionssuitable for complex formation. The amount of standard complex formationmay be quantified by various methods, but preferably by photometricmeans. Quantities of CD74-ROS fusion polypeptide expressed in subject,control, and disease samples from biopsied tissues are compared with thestandard values. Deviation between standard and subject valuesestablishes the parameters for diagnosing disease.

Peptide & Nucleotide Assays.

Similarly, AQUA peptides for the detection/quantification of expressedmutant ROS polypeptide in a biological sample comprising cells from atumor may be prepared and used in standard AQUA assays, as described indetail in Section E above. Accordingly, in some preferred embodiments ofthe methods of the invention, the CD74-ROS fusion polypeptide-specificreagent comprises a heavy isotope labeled phosphopeptide (AQUA peptide)corresponding to a peptide sequence comprising the fusion junction ofCD74-ROS fusion polypeptide, as described above in Section E.

Mutant ROS kinase polypeptide-specific reagents useful in practicing themethods of the invention may also be mRNA, oligonucleotide or DNA probesthat can directly hybridize to, and detect, fusion or truncatedpolypeptide expression transcripts in a biological sample. Such probesare discussed in detail in Section B above. Briefly, and by way ofexample, formalin-fixed, paraffin-embedded patient samples may be probedwith a fluorescein-labeled RNA probe followed by washes with formamide,SSC and PBS and analysis with a fluorescent microscope.

Polynucleotides encoding mutant ROS kinase polypeptide may also be usedfor diagnostic purposes. The polynucleotides that may be used includeoligonucleotide sequences, antisense RNA and DNA molecules, and PNAs.The polynucleotides may be used to detect and quantitate gene expressionin biopsied tissues in which expression of CD74-ROS fusion polypeptideor truncated ROS polypeptide may be correlated with disease. Thediagnostic assay may be used to distinguish between absence, presence,and excess expression of CD74-ROS fusion polypeptide, and to monitorregulation of CD74-ROS fusion polypeptide levels during therapeuticintervention.

In one preferred embodiment, hybridization with PCR probes which arecapable of detecting polynucleotide sequences, including genomicsequences, encoding CD74-ROS fusion polypeptide or truncated ROS kinasepolypeptide or closely related molecules, may be used to identifynucleic acid sequences that encode mutant ROS polypeptide. Theconstruction and use of such probes is described in Section B above. Thespecificity of the probe, whether it is made from a highly specificregion, e.g., 10 unique nucleotides in the fusion junction, or a lessspecific region. e.g., the 3′ coding region, and the stringency of thehybridization or amplification (maximal, high, intermediate, or low)will determine whether the probe identifies only naturally occurringsequences encoding mutant ROS kinase polypeptide, alleles, or relatedsequences.

Probes may also be used for the detection of related sequences, andshould preferably contain at least 50% of the nucleotides from any ofthe mutant ROS polypeptide encoding sequences. The hybridization probesof the subject invention may be DNA or RNA and derived from thenucleotide sequences of SEQ ID NOs: 2, most preferably encompassing thefusion junction, or from genomic sequence including promoter, enhancerelements, and introns of the naturally occurring CD74 and ROSpolypeptides, as further described in Section B above.

A CD74-ROS fusion polynucleotide or truncated ROS polynucleotide of theinvention may be used in Southern or northern analysis, dot blot, orother membrane-based technologies; in PCR technologies; or in dip stick,pin, ELISA or chip assays utilizing fluids or tissues from patientbiopsies to detect altered mutant ROS kinase polypeptide expression.Such qualitative or quantitative methods are well known in the art. In aparticular aspect, the nucleotide sequences encoding mutant ROSpolypeptide may be useful in assays that detect activation or inductionof various cancers, including cancers of the lung including NSCLC.Mutant ROS polynucleotides may be labeled by standard methods, and addedto a fluid or tissue sample from a patient under conditions suitable forthe formation of hybridization complexes. After a suitable incubationperiod, the sample is washed and the signal is quantitated and comparedwith a standard value. If the amount of signal in the biopsied orextracted sample is significantly altered from that of a comparablecontrol sample, the nucleotide sequences have hybridized with nucleotidesequences in the sample, and the presence of altered levels ofnucleotide sequences encoding CD74-ROS fusion polypeptide or truncatedROS kinase polypeptide in the sample indicates the presence of theassociated disease. Such assays may also be used to evaluate theefficacy of a particular therapeutic treatment regimen in animalstudies, in clinical trials, or in monitoring the treatment of anindividual patient.

In order to provide a basis for the diagnosis of disease characterizedby expression of mutant ROS polypeptide, a normal or standard profilefor expression is established. This may be accomplished by combiningbody fluids or cell extracts taken from normal subjects, either animalor human, with a sequence, or a fragment thereof, which encodes CD74-ROSfusion polypeptide or truncated ROS kinase polypeptide, under conditionssuitable for hybridization or amplification. Standard hybridization maybe quantified by comparing the values obtained from normal subjects withthose from an experiment where a known amount of a substantiallypurified polynucleotide is used. Standard values obtained from normalsamples may be compared with values obtained from samples from patientswho are symptomatic for disease. Deviation between standard and subjectvalues is used to establish the presence of disease.

Once disease is established and a treatment protocol is initiated,hybridization assays may be repeated on a regular basis to evaluatewhether the level of expression in the patient begins to approximatethat which is observed in the normal patient. The results obtained fromsuccessive assays may be used to show the efficacy of treatment over aperiod ranging from several days to months.

Additional diagnostic uses for mutant ROS polynucleotides of theinvention may involve the use of polymerase chain reaction (PCR),another preferred assay format that is standard to those of skill in theart. See, e.g., MOLECULAR CLONING, A LABORATORY MANUAL, 2nd, edition.Sambrook, J., Fritsch, E. F, and Maniatis. T., eds., Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y. (1989). PCR oligomers may bechemically synthesized, generated enzymatically, or produced from arecombinant source. Oligomers will preferably consist of two nucleotidesequences, one with sense orientation (5′ to 3′) and another withantisense (3′ to 5′), employed under optimized conditions foridentification of a specific gene or condition. The same two oligomers,nested sets of oligomers, or even a degenerate pool of oligomers may beemployed under less stringent conditions for detection and/orquantitation of closely related DNA or RNA sequences.

Methods which may also be used to quantitate the expression of CD74-ROSfusion polypeptide or truncated ROS kinase polypeptide includeradiolabeling or biotinylating nucleotides, coamplification of a controlnucleic acid, and standard curves onto which the experimental resultsare interpolated (Melby et al., J. Immunol. Methods, 159: 235-244(1993); Duplaa et al. Anal. Biochem. 229-236 (1993)). The speed ofquantitation of multiple samples may be accelerated by running the assayin an ELISA format where the oligomer of interest is presented invarious dilutions and a spectrophotometric or colorimetric responsegives rapid quantitation.

In another embodiment of the invention, the mutant ROS polynucleotidesof the invention may be used to generate hybridization probes which areuseful for mapping the naturally occurring genomic sequence. Thesequences may be mapped to a particular chromosome or to a specificregion of the chromosome using well known techniques. Such techniquesinclude fluorescence in-situ hybridization (FISH). FACS, or artificialchromosome constructions, such as yeast artificial chromosomes,bacterial artificial chromosomes, bacterial PI constructions or singlechromosome cDNA libraries, as reviewed in Price, C. M., Blood Rev. 7:127-134 (1993), and Trask, B. J., Trends Genet. 7: 149-154 (1991).

In one preferred embodiment. FISH is employed (as described in Verma etal. HUMAN CHROMOSOMES: A MANUAL OF BASIC TECHNIQUES, Pergamon Press, NewYork, N.Y. (1988)) and may be correlated with other physical chromosomemapping techniques and genetic map data. Examples of genetic map datacan be found in the 1994 Genome Issue of Science (265: 1981f).Correlation between the location of the gene encoding CD74-ROS fusionpolypeptide or truncated ROS polypeptide on a physical chromosomal mapand a specific disease, or predisposition to a specific disease, mayhelp delimit the region of DNA associated with that genetic disease. Thenucleotide sequences of the subject invention may be used to detectdifferences in gene sequences between normal, carrier, or affectedindividuals.

In situ hybridization of chromosomal preparations and physical mappingtechniques such as linkage analysis using established chromosomalmarkers may be used for extending genetic maps. Often the placement of agene on the chromosome of another mammalian species, such as mouse, mayreveal associated markers even if the number or arm of a particularhuman chromosome is not known. New sequences can be assigned tochromosomal arms, or parts thereof, by physical mapping. This providesvaluable information to investigators searching for disease genes usingpositional cloning or other gene discovery techniques. Once the diseaseor syndrome has been crudely localized by genetic linkage to aparticular genomic region, for example, AT to 11 q22-23 (Gatti et al.,Nature 336: 577-580 (1988)), any sequences mapping to that area mayrepresent associated or regulatory genes for further investigation. Thenucleotide sequence of the subject invention may also be used to detectdifferences in the chromosomal location due to translocation, inversion,etc., among normal, carrier, or affected individuals.

Biological Samples

Biological samples useful in the practice of the methods of theinvention may be obtained from any mammal in which a cancercharacterized by the presence of a CD74-ROS fusion polypeptide is ormight be present or developing. In one embodiment, the mammal is ahuman, and the human may be a candidate for a ROS-inhibitingtherapeutic, for the treatment of a lung cancer. e.g. NSCLC. The humancandidate may be a patient currently being treated with, or consideredfor treatment with, a ROS kinase inhibitor. In another embodiment, themammal is large animal, such as a horse or cow, while in otherembodiments, the mammal is a small animal, such as a dog or cat, all ofwhich are known to develop cancers, including lung cancers.

Any biological sample comprising cells (or extracts of cells) from amammalian cancer is suitable for use in the methods of the invention. Inone embodiment, the biological sample comprises cells obtained from atumor biopsy. The biopsy may be obtained, according to standard clinicaltechniques, from primary tumors occurring in an organ of a mammal, or bysecondary tumors that have metastasized in other tissues. In anotherembodiment, the biological sample comprises cells obtained from a fineneedle aspirate taken from a tumor, and techniques for obtaining suchaspirates are well known in the art (see Cristallini et al., Acta Cytol.36(3): 416-22 (1992)).

The biological sample may also comprise cells obtained from an effusion,such as a pleural effusion. Pleural effusions (liquid that forms outsidethe lung in the thoracic cavity and which contains cancerous cells) areknown to form in many patients with advanced lung cancer (includingNSCLC), and the presence of such effusion is predictive of a pooroutcome and short survival time. Standard techniques for obtainingpleural effusion samples have been described and are well known in theart (see Sahn, Clin Chest Med 3(2): 443-52 (1982)). Circulating tumorcells may also be obtained from serum using tumor markers, cytokeratinprotein markers or other methods of negative selection as described (seeMa et al., Anticancer Res. 23(1A): 49-62 (2003)). Serum and bone marrowsamples may be particularly preferred for patients with leukemia.Aberrant expression of ROS has been observed in a glioblastoma. SeeCharest et al., supra.

A biological sample may comprise cells (or cell extracts) from a cancerin which CD74-ROS fusion polypeptide or truncated ROS kinase polypeptideis expressed and/or activated but wild type ROS kinase is not.Alternatively, the sample may comprise cells from a cancer in which bothmutant ROS polypeptide and wild type ROS kinase are expressed and/oractivated, or in which wild type ROS kinase and/or CD74 are expressedand/or active, but mutant ROS polypeptide is not.

Cellular extracts of the foregoing biological samples may be prepared,either crude or partially (or entirely) purified, in accordance withstandard techniques, and used in the methods of the invention.Alternatively, biological samples comprising whole cells may be utilizedin preferred assay formats such as immunohistochemistry (IHC), flowcytometry (FC), and immunofluorescence (IF), as further described above.Such whole-cell assays are advantageous in that they minimizemanipulation of the tumor cell sample and thus reduce the risks ofaltering the in vivo signaling/activation state of the cells and/orintroducing artifact signals. Whole cell assays are also advantageousbecause they characterize expression and signaling only in tumor cells,rather than a mixture of tumor and normal cells.

In practicing the disclosed method for determining whether a compoundinhibits progression of a tumor characterized by a CD74-ROStranslocation and/or fusion polypeptide, biological samples comprisingcells from mammalian xenografts (or bone marrow transplants) may also beadvantageously employed. Preferred xenografts (or transplant recipients)are small mammals, such as mice, harboring human tumors (or leukemias)that express a mutant ROS kinase polypeptide. Xenografts harboring humantumors are well known in the art (see Kal, Cancer Treat Res. 72: 155-69(1995)) and the production of mammalian xenografts harboring humantumors is well described (see Winograd et al., In Vivo. 1(1): 1-13(1987)). Similarly the generation and use of bone marrow transplantmodels is well described (see, e.g., Schwaller, et al., EMBO J. 17:5321-333 (1998); Kelly et al., Blood 99: 310-318 (2002)). By “cancercharacterized by” a CD74-ROS translocation and/or fusion polypeptide ismeant a cancer in which such mutant ROS gene and/or expressedpolypeptide are present, as compared to a cancer in which suchtranslocation and/or fusion polypeptide are not present.

In assessing mutant ROS polynucleotide presence or polypeptideexpression in a biological sample comprising cells from a mammaliancancer tumor, a control sample representing a cell in which suchtranslocation and/or fusion protein do not occur may desirably beemployed for comparative purposes. Ideally, the control sample comprisescells from a subset of the particular cancer (e.g. NSCLC) that isrepresentative of the subset in which the mutation (e.g. CD74-ROStranslocation) does not occur and/or the fusion polypeptide is notexpressed. Comparing the level in the control sample versus the testbiological sample thus identifies whether the mutant polynucleotideand/or polypeptide is/are present. Alternatively, since CD74-ROS fusionpolynucleotide and/or polypeptide may not be present in the majority ofcancers, any tissue that similarly does not express mutant ROSpolypeptide (or harbor the mutant polynucleotide) may be employed as acontrol.

The methods described below will have valuable diagnostic utility forcancers characterized by mutant ROS polynucleotide and/or polypeptide,and treatment decisions pertaining to the same. For example, biologicalsamples may be obtained from a subject that has not been previouslydiagnosed as having a cancer characterized by since a CD74-ROStranslocation and/or fusion polypeptide, nor has yet undergone treatmentfor such cancer, and the method is employed to diagnostically identify atumor in such subject as belonging to a subset of tumors (e.g. NSCLCtumors) in which mutant ROS polynucleotide and/or polypeptide ispresent/expressed.

Alternatively, a biological sample may be obtained from a subject thathas been diagnosed as having a cancer driven by one type of kinase, suchas EFGR, and has been receiving therapy, such as EGFR inhibitor therapy(e.g. Tarceva™, Iressa™) for treatment of such cancer, and the method ofthe invention is employed to identify whether the subject's tumor isalso characterized by a CD74-ROS translocation and/or fusionpolypeptide, and is therefore likely to fully respond to the existingtherapy and/or whether alternative or additional ROS kinase-inhibitingtherapy is desirable or warranted. The methods of the invention may alsobe employed to monitor the progression or inhibition of a mutant ROSpolypeptide-expressing cancer following treatment of a subject with acomposition comprising a ROS kinase-inhibiting therapeutic orcombination of therapeutics.

Such diagnostic assay may be carried out subsequent to or prior topreliminary evaluation or surgical surveillance procedures. Theidentification method of the invention may be advantageously employed asa diagnostic to identify patients having cancer, such as NSCLC, drivenby the CD74-ROS fusion protein, which patients would be most likely torespond to therapeutics targeted at inhibiting ROS kinase activity. Theability to select such patients would also be useful in the clinicalevaluation of efficacy of future ROS-targeted therapeutics as well as inthe future prescription of such drugs to patients.

Diagnostics.

The ability to selectively identify cancers in which a CD74-ROStranslocation and/or fusion polypeptide is/are present enables importantnew methods for accurately identifying such tumors for diagnosticpurposes, as well as obtaining information useful in determining whethersuch a tumor is likely to respond to a ROS-inhibiting therapeuticcomposition, or likely to be partially or wholly non-responsive to aninhibitor targeting a different kinase when administered as a singleagent for the treatment of the cancer.

Accordingly, in one embodiment, the invention provides a method fordetecting the presence of a mutant ROS polynucleotide and/or polypeptidein a cancer, the method comprising the steps of: (a) obtaining abiological sample from a patient having cancer; and (b) utilizing atleast one reagent that detects a mutant ROS polynucleotide orpolypeptide of the invention to determine whether a CD74-ROS fusionpolynucleotide and/or polypeptide is/are present in the biologicalsample.

In some preferred embodiments, the cancer is a lung cancer, such asnon-small cell lung carcinoma (NSCLC). In other preferred embodiments,the presence of a mutant ROS kinase polypeptide identifies a cancer thatis likely to respond to a composition comprising at least one ROSkinase-inhibiting therapeutic.

In some preferred embodiments, the diagnostic methods of the inventionare implemented in a flow-cytometry (FC), immuno-histochemistry (IHC),or immuno-fluorescence (IF) assay format. In another preferredembodiment, the activity of the CD74-ROS fusion polypeptide is detected.In other preferred embodiments, the diagnostic methods of the inventionare implemented in a fluorescence in situ hybridization (FISH) orpolymerase chain reaction (PCR) assay format.

The invention further provides a method for determining whether acompound inhibits the progression of a cancer characterized by aCD74-ROS fusion polynucleotide or polypeptide, said method comprisingthe step of determining whether said compound inhibits the expressionand/or activity of said CD74-ROS fusion in said cancer. In one preferredembodiment, inhibition of expression and/or activity of the CD74-ROSfusion polypeptide is determined using at least one reagent that detectsan CD74-ROS fusion polynucleotide or polypeptide of the invention.Compounds suitable for inhibition of ROS kinase activity are discussedin more detail in Section G below.

Mutant ROS polynucleotide probes and polypeptide-specific reagentsuseful in the practice of the methods of the invention are described infurther detail in sections B and D above. In one preferred embodiment,the CD74-ROS fusion polypeptide-specific reagent comprises a fusionpolypeptide-specific antibody. In another preferred embodiment, thefusion polypeptide-specific reagent comprises a heavy-isotope labeledphosphopeptide (AQUA peptide) corresponding to the fusion junction ofCD74-ROS fusion polypeptide

The methods of the invention described above may also optionallycomprise the step of determining the level of expression or activationof other kinases, such as wild type ROS and EGFR, or other downstreamsignaling molecules in said biological sample. Profiling both CD74-ROSfusion polypeptide expression/activation and expression/activation ofother kinases and pathways in a given biological sample can providevaluable information on which kinase(s) and pathway(s) is/are drivingthe disease, and which therapeutic regime is therefore likely to be ofmost benefit.

Compound Screening.

The discovery of the novel CD74-ROS fusion polypeptides described hereinalso enables the development of new compounds that inhibit the activityof these mutant ROS proteins, particularly their ROS kinase activity.Accordingly, the invention also provides, in part, a method fordetermining whether a compound inhibits the progression of a cancercharacterized by a CD74-ROS fusion polynucleotide and/or polypeptide,said method comprising the step of determining whether said compoundinhibits the expression and/or activity of said CD74-ROS fusionpolypeptide in said cancer. In one preferred embodiment, inhibition ofexpression and/or activity of the CD74-ROS fusion polypeptide isdetermined using at least one reagent that detects a mutant ROSpolynucleotide and/or mutant ROS polypeptide of the invention. Preferredreagents of the invention have been described above. Compounds suitablefor the inhibition of ROS kinase activity are described in more detailin Section G below.

The compound may, for example, be a kinase inhibitor, such as a smallmolecule or antibody inhibitor. It may be a pan-kinase inhibitor withactivity against several different kinases, or a kinase-specificinhibitor. ROS kinase-inhibiting compounds are discussed in furtherdetail in Section G below. Patient biological samples may be takenbefore and after treatment with the inhibitor and then analyzed, usingmethods described above, for the biological effect of the inhibitor onROS kinase activity, including the phosphorylation of downstreamsubstrate protein. Such a pharmacodynamic assay may be useful indetermining the biologically active dose of the drug that may bepreferable to a maximal tolerable dose. Such information would also beuseful in submissions for drug approval by demonstrating the mechanismof drug action. Identifying compounds with such desired inhibitorycharacteristics is further described in Section G below.

G. Therapeutic Inhibition of Cancers.

In accordance with the present invention, it has now been shown that theCD74-ROS fusion polypeptide occurs in at least one subgroup of humanNSCLC. Accordingly, the progression of a mammalian cancer (e.g. NSCLC)in which CD74-ROS fusion protein is expressed may be inhibited, in vivo,by inhibiting the activity of ROS kinase in such cancer. ROS activity incancers characterized by expression of a mutant ROS kinase may beinhibited by contacting the cancer (e.g. a tumor) with a ROSkinase-inhibiting therapeutic. Accordingly, the invention provides, inpart, a method for inhibiting the progression of a CD74-ROS fusionpolypeptide-expressing cancer by inhibiting the expression and/oractivity of ROS kinase in the cancer.

A ROS kinase-inhibiting therapeutic may be any composition comprising atleast one compound, biological or chemical, which inhibits, directly orindirectly, the expression and/or activity of ROS kinase in vivo,including the exemplary classes of compounds described below. Suchcompounds include therapeutics that act directly on ROS kinase itself,or on proteins or molecules that modify the activity of ROS, or that actindirectly by inhibiting the expression of ROS. Such compositions alsoinclude compositions comprising only a single ROS kinase inhibitingcompound, as well as compositions comprising multiple therapeutics(including those against other RTKs), which may also include anon-specific therapeutic agent like a chemotherapeutic agent or generaltranscription inhibitor.

Small-Molecule Inhibitors.

In some preferred embodiments, a ROS-inhibiting therapeutic useful inthe practice of the methods of the invention is a targeted, smallmolecule inhibitor. Small molecule targeted inhibitors are a class ofmolecules that typically inhibit the activity of their target enzyme byspecifically, and often irreversibly, binding to the catalytic site ofthe enzyme, and/or binding to an ATP-binding cleft or other binding sitewithin the enzyme that prevents the enzyme from adopting a conformationnecessary for its activity. An exemplary small-molecule targeted kinaseinhibitor is Gleevec® (Imatinib, STI-571), which inhibits CSF1R andBCR-ABL, and its properties have been well described. See Dewar et al.,Blood 105(8): 3127-32 (2005).

Small molecule inhibitors may be rationally designed using X-raycrystallographic or computer modeling of ROS kinase three-dimensionalstructure, or may found by high throughput screening of compoundlibraries for inhibition of ROS. Such methods are well known in the art,and have been described. Specificity of ROS inhibition may be confirmed,for example, by examining the ability of such compound to inhibit ROSactivity, but not other kinase activity, in a panel of kinases, and/orby examining the inhibition of ROS activity in a biological samplecomprising NSCLC tumor cells, as described above. Such screening methodsare further described below.

Antibody Inhibitors.

ROS kinase-inhibiting therapeutics useful in the methods of theinvention may also be targeted antibodies that specifically bind tocritical catalytic or binding sites or domains required for ROSactivity, and inhibit the kinase by blocking access of ligands,substrates or secondary molecules to a and/or preventing the enzyme fromadopting a conformation necessary for its activity. The production,screening, and therapeutic use of humanized target-specific antibodieshas been well-described. See Merluzzi et al., Adv Clin Path. 4(2): 77-85(2000). Commercial technologies and systems, such as Morphosys. Inc.'sHuman Combinatorial Antibody Library (HuCAL®), for the high-throughputgeneration and screening of humanized target-specific inhibitingantibodies are available.

The production of various anti-receptor kinase targeted antibodies andtheir use to inhibit activity of the targeted receptor has beendescribed. See, e.g. U.S. Patent Publication No. 20040202655.“Antibodies to IGF-I Receptor for the Treatment of Cancers,” Oct. 14,2004, Morton et al.; U.S. Patent Publication No. 20040086503, “Humananti-Epidermal Growth Factor Receptor Single-Chain Antibodies.” Apr. 15,2004, Raisch et al.; U.S. Patent Publication No. 20040033543, “Treatmentof Renal Carcinoma Using Antibodies Against the EGFr,” Feb. 19, 2004,Schwab et. al. Standardized methods for producing, and using, receptortyrosine kinase activity-inhibiting antibodies are known in the art.See, e.g., European Patent No. EP1423428, “Antibodies that BlockReceptor Tyrosine Kinase Activation, Methods of Screening for and UsesThereof,” Jun. 2, 2004. Borges et al.

Phage display approaches may also be employed to generate ROS-specificantibody inhibitors, and protocols for bacteriophage libraryconstruction and selection of recombinant antibodies are provided in thewell-known reference text CURRENT PROTOCOLS IN IMMUNOLOGY, Colligan etal. (Eds.). John Wiley & Sons, Inc. (1992-2000). Chapter 17, Section17.1. See also U.S. Pat. No. 6,319,690, Nov. 20, 2001, Little et al.;U.S. Pat. No. 6,300,064, Oct. 9, 2001, Knappik et al.; U.S. Pat. No.5,840,479, Nov. 24, 1998, Little et al.; U.S. Patent Publication No.20030219839, Nov. 27, 2003, Bowdish et al.

A library of antibody fragments displayed on the surface ofbacteriophages may be produced (see, e.g. U.S. Pat. No. 6,300,064, Oct.9, 2001. Knappik et al.) and screened for binding to a soluble dimericform of a receptor protein tyrosine kinase (like ROS). An antibodyfragment that binds to the soluble dimeric form of the RTK used forscreening is identified as a candidate molecule for blockingconstitutive activation of the target RTK in a cell. See European PatentNo. EP1423428, Borges et al., supra.

ROS-binding targeted antibodies identified in screening of antibodylibraries as describe above may then be further screened for theirability to block the activity of ROS, both in vitro kinase assay and invivo in cell lines and/or tumors. ROS inhibition may be confirmed, forexample, by examining the ability of such antibody therapeutic toinhibit ROS kinase activity, but not other kinase activity, in a panelof kinases, and/or by examining the inhibition of ROS activity in abiological sample comprising cancer cells, as described above. Methodsfor screening such compounds for ROS kinase inhibition are furtherdescribed above.

Indirect Inhibitors.

ROS-inhibiting compounds useful in the practice of the disclosed methodsmay also be compounds that indirectly inhibit ROS activity by inhibitingthe activity of proteins or molecules other than ROS kinase itself. Suchinhibiting therapeutics may be targeted inhibitors that modulate theactivity of key regulatory kinases that phosphorylate orde-phosphorylate (and hence activate or deactivate) ROS itself orinterfere with binding of ligands. As with other receptor tyrosinekinases, ROS regulates downstream signaling through a network of adaptorproteins and downstream kinases. As a result, induction of cell growthand survival by ROS activity may be inhibited by targeting theseinteracting or downstream proteins.

ROS kinase activity may also be indirectly inhibited by using a compoundthat inhibits the binding of an activating molecule necessary for ROS toadopt its active conformation. For example, the production and use ofanti-PDGF antibodies has been described. See U.S. Patent Publication No.20030219839. “Anti-PDGF Antibodies and Methods for Producing EngineeredAntibodies.” Bowdish et al. Inhibition of ligand (PDGF) binding to thereceptor directly down-regulates the receptor activity.

Indirect inhibitors of ROS activity may be rationally designed usingX-ray crystallographic or computer modeling of ROS three dimensionalstructure, or may found by high throughput screening of compoundlibraries for inhibition of key upstream regulatory enzymes and/ornecessary binding molecules, which results in inhibition of ROS kinaseactivity. Such approaches are well known in the art, and have beendescribed. ROS inhibition by such therapeutics may be confirmed, forexample, by examining the ability of the compound to inhibit ROSactivity, but not other kinase activity, in a panel of kinases, and/orby examining the inhibition of ROS activity in a biological samplecomprising cancer cells, e.g. NSCLC cells, as described above. Methodsfor identifying compounds that inhibit a cancer characterized by aCD74-ROS translocation and/or fusion polypeptide, and/or truncated ROSpolynucleotide and/or polypeptide, are further described below.

Anti-Sense and/or Transcription Inhibitors.

ROS inhibiting therapeutics may also comprise anti-sense and/ortranscription inhibiting compounds that inhibit ROS kinase activity byblocking transcription of the gene encoding ROS and/or the CD74-ROSfusion gene. The inhibition of various receptor kinases, includingVEGFR. EGFR, and IGFR, and FGFR, by antisense therapeutics for thetreatment of cancer has been described. See, e.g., U.S. Pat. Nos.6,734,017; 6,710,174, 6,617,162; 6,340,674; 5,783,683; 5,610,288.

Antisense oligonucleotides may be designed, constructed, and employed astherapeutic agents against target genes in accordance with knowntechniques. See, e.g. Cohen, J., Trends in Pharmacol. Sci. 10(11):435-437 (1989); Marcus-Sekura, Anal. Biochem. 172: 289-295 (1988);Weintraub, H., Sci. AM. pp. 40-46 (1990); Van Der Krol et al.,BioTechniques 6(10): 958-976 (1988); Skorski et al., Proc. Natl. AcadSci. USA (1994) 91: 4504-4508. Inhibition of human carcinoma growth invivo using an antisense RNA inhibitor of EGFR has recently beendescribed. See U.S. Patent Publication No. 20040047847, “Inhibition ofHuman Squamous Cell Carcinoma Growth In vivo by Epidermal Growth FactorReceptor Antisense RNA Transcribed from a Pol III Promoter,” Mar. 11,2004. He et al. Similarly, a ROS-inhibiting therapeutic comprising atleast one antisense oligonucleotide against a mammalian ROS gene (seeFIG. 4 (SEQ ID NO: 8) or CD74-ROS fusion polynucleotide or truncated ROSpolynucleotide (see FIG. 2 (SEQ ID NOs: 2) or truncated may be preparedaccording to methods described above. Pharmaceutical compositionscomprising ROS-inhibiting antisense compounds may be prepared andadministered as further described below.

Small Interfering RNA.

Small interfering RNA molecule (siRNA) compositions, which inhibittranslation, and hence activity, of ROS through the process of RNAinterference, may also be desirably employed in the methods of theinvention. RNA interference, and the selective silencing of targetprotein expression by introduction of exogenous small double-strandedRNA molecules comprising sequence complimentary to mRNA encoding thetarget protein, has been well described. See, e.g. U.S. PatentPublication No. 20040038921, “Composition and Method for InhibitingExpression of a Target Gene,” Feb. 26, 2004, Kreutzer et al.; U.S.Patent Publication No. 20020086356, “RNA Sequence-Specific Mediators ofRNA Interference,” Jun. 12, 2003, Tuschl et al.; U.S. Patent Publication20040229266. “RNA Interference Mediating Small RNA Molecules.” Nov. 18,2004, Tuschl et. al.

For example, as described in Example 3, siRNA-mediated silencing ofexpression of the CD74-ROS fusion protein may be effected in a humanNSCLC cell line expressing the fusion protein.

Double-stranded RNA molecules (dsRNA) have been shown to block geneexpression in a highly conserved regulatory mechanism known as RNAinterference (RNAi). Briefly, the RNAse III Dicer processes dsRNA intosmall interfering RNAs (siRNA) of approximately 22 nucleotides, whichserve as guide sequences to induce target-specific mRNA cleavage by anRNA-induced silencing complex RISC (see Hammond et al., Nature (2000)404: 293-296). RNAi involves a catalytic-type reaction whereby newsiRNAs are generated through successive cleavage of longer dsRNA. Thus,unlike antisense, RNAi degrades target RNA in a non-stoichiometricmanner. When administered to a cell or organism, exogenous dsRNA hasbeen shown to direct the sequence-specific degradation of endogenousmessenger RNA (mRNA) through RNAi.

A wide variety of target-specific siRNA products, including vectors andsystems for their expression and use in mammalian cells, are nowcommercially available. See. e.g. Promega. Inc. (www.promega.com);Dharmacon, Inc. (www.dharmacon.com). Detailed technical manuals on thedesign, construction, and use of dsRNA for RNAi are available. See, e.g.Dharmacon's “RNAi Technical Reference & Application Guide”; Promega's“RNAi: A Guide to Gene Silencing.” ROS-inhibiting siRNA products arealso commercially available, and may be suitably employed in the methodof the invention. See, e.g. Dharmacon, Inc., Lafayette, Colo. (Cat Nos.M-003162-03, MU-003162-03, D-003162-07 thru -10 (siGENOME™SMARTselection and SMARTpool® siRNAs).

It has recently been established that small dsRNA less than 49nucleotides in length, and preferably 19-25 nucleotides, comprising atleast one sequence that is substantially identical to part of a targetmRNA sequence, and which dsRNA optimally has at least one overhang of1-4 nucleotides at an end, are most effective in mediating RNAi inmammals. See U.S. Patent Publication No. 20040038921, Kreutzer et al.,supra; U.S. Patent Publication No. 20040229266, Tuschl et al., supra.The construction of such dsRNA, and their use in pharmaceuticalpreparations to silence expression of a target protein, in vivo, aredescribed in detail in such publications.

If the sequence of the gene to be targeted in a mammal is known, 21-23nt RNAs, for example, can be produced and tested for their ability tomediate RNAi in a mammalian cell, such as a human or other primate cell.Those 21-23 nt RNA molecules shown to mediate RNAi can be tested, ifdesired, in an appropriate animal model to further assess their in vivoeffectiveness. Target sites that are known, for example target sitesdetermined to be effective target sites based on studies with othernucleic acid molecules, for example ribozymes or antisense, or thosetargets known to be associated with a disease or condition such as thosesites containing mutations or deletions, can be used to design siRNAmolecules targeting those sites as well.

Alternatively, the sequences of effective dsRNA can be rationallydesigned/predicted screening the target mRNA of interest for targetsites, for example by using a computer folding algorithm. The targetsequence can be parsed in silico into a list of all fragments orsubsequences of a particular length, for example 23 nucleotidefragments, using a custom Perl script or commercial sequence analysisprograms such as Oligo, MacVector, or the GCG Wisconsin Package.

Various parameters can be used to determine which sites are the mostsuitable target sites within the target RNA sequence. These parametersinclude but are not limited to secondary or tertiary RNA structure, thenucleotide base composition of the target sequence, the degree ofhomology between various regions of the target sequence, or the relativeposition of the target sequence within the RNA transcript. Based onthese determinations, any number of target sites within the RNAtranscript can be chosen to screen siRNA molecules for efficacy, forexample by using in vitro RNA cleavage assays, cell culture, or animalmodels. See, e.g., U.S. Patent Publication No. 20030170891, Sep. 11,2003, McSwiggen J. An algorithm for identifying and selecting RNAitarget sites has also recently been described. See U.S. PatentPublication No. 20040236517. “Selection of Target Sites for AntisenseAttack of RNA,” Nov. 25, 2004, Drlica et al.

Commonly used gene transfer techniques include calcium phosphate,DEAE-dextran, electroporation and microinjection and viral methods(Graham et al. (1973) Virol. 52: 456; McCutchan et al., (1968), J. Natl.Cancer Inst. 41: 351; Chu et al. (1987). Nucl. Acids Res. 15: 1311;Fraley et al. (1980), J. Biol. Chem. 255: 10431; Capecchi (1980), Cell22: 479). DNA may also be introduced into cells using cationic liposomes(Feigner et al. (1987), Proc. Natl. Acad. Sci USA 84: 7413).Commercially available cationic lipid formulations include Tfx 50(Promega) or Lipofectamin 200 (Life Technologies). Alternatively, viralvectors may be employed to deliver dsRNA to a cell and mediate RNAi. SeeU.S Patent Publication No. 20040023390, “siRNA-mediated Gene Silencingwith Viral Vectors,” Feb. 4, 2004, Davidson et at.

Transfection and vector/expression systems for RNAi in mammalian cellsare commercially available and have been well described. See, e.g.Dharmacon, Inc., DharmaFECT™ system: Promega, Inc., siSTRIKE™ U6 Hairpinsystem; see also Gou et al. (2003) FEBS. 548, 113-118: Sui, G. et al. ADNA vector-based RNAi technology to suppress gene expression inmammalian cells (2002) Proc. Natl. Acad. Sci. 99, 5515-5520; Yu et al.(2002) Proc. Natl. Acad. Sci. 99, 6047-6052: Paul, C. et al. (2002)Nature Biotechnology 19, 505-508: McManus et al. (2002) RNA 8, 842-850.

siRNA interference in a mammal using prepared dsRNA molecules may thenbe effected by administering a pharmaceutical preparation comprising thedsRNA to the mammal. The pharmaceutical composition is administered in adosage sufficient to inhibit expression of the target gene, dsRNA cantypically be administered at a dosage of less than 5 mg dsRNA perkilogram body weight per day, and is sufficient to inhibit or completelysuppress expression of the target gene. In general a suitable dose ofdsRNA will be in the range of 0.01 to 2.5 milligrams per kilogram bodyweight of the recipient per day, preferably in the range of 0.1 to 200micrograms per kilogram body weight per day, more preferably in therange of 0.1 to 100 micrograms per kilogram body weight per day, evenmore preferably in the range of 1.0 to 50 micrograms per kilogram bodyweight per day, and most preferably in the range of 1.0 to 25 microgramsper kilogram body weight per day. A pharmaceutical compositioncomprising the dsRNA is administered once daily, or in multiplesub-doses, for example, using sustained release formulations well knownin the art. The preparation and administration of such pharmaceuticalcompositions may be carried out accordingly to standard techniques, asfurther described below.

Such dsRNA may then be used to inhibit ROS expression and activity in acancer, by preparing a pharmaceutical preparation comprising atherapeutically-effective amount of such dsRNA, as described above, andadministering the preparation to a human subject having a cancerexpressing CD74-ROS fusion protein or truncated ROS kinase polypeptide,for example, via direct injection to the tumor. The similar inhibitionof other receptor tyrosine kinases, such as VEGFR and EGFR using siRNAinhibitors has recently been described. See U.S. Patent Publication No.20040209832, Oct. 21, 2004, McSwiggen et al.; U.S. Patent PublicationNo. 20030170891, Sep. 11, 2003, McSwiggen; U.S. Patent Publication No.20040175703, Sep. 9, 2004, Kreutzer et al.

Therapeutic Compositions; Administration.

ROS kinase-inhibiting therapeutic compositions useful in the practice ofthe methods of the invention may be administered to a mammal by anymeans known in the art including, but not limited to oral or peritonealroutes, including intravenous, intramuscular, intraperitoneal,subcutaneous, transdermal, airway (aerosol), rectal, vaginal and topical(including buccal and sublingual) administration.

For oral administration, a ROS-inhibiting therapeutic will generally beprovided in the form of tablets or capsules, as a powder or granules, oras an aqueous solution or suspension. Tablets for oral use may includethe active ingredients mixed with pharmaceutically acceptable excipientssuch as inert diluents, disintegrating agents, binding agents,lubricating agents, sweetening agents, flavoring agents, coloring agentsand preservatives. Suitable inert diluents include sodium and calciumcarbonate, sodium and calcium phosphate, and lactose, while corn starchand alginic acid are suitable disintegrating agents. Binding agents mayinclude starch and gelatin, while the lubricating agent, if present,will generally be magnesium stearate, stearic acid or talc. If desired,the tablets may be coated with a material such as glyceryl monostearateor glyceryl distearate, to delay absorption in the gastrointestinaltract.

Capsules for oral use include hard gelatin capsules in which the activeingredient is mixed with a solid diluent, and soft gelatin capsuleswherein the active ingredients is mixed with water or an oil such aspeanut oil, liquid paraffin or olive oil. For intramuscular,intraperitoneal, subcutaneous and intravenous use, the pharmaceuticalcompositions of the invention will generally be provided in sterileaqueous solutions or suspensions, buffered to an appropriate pH andisotonicity. Suitable aqueous vehicles include Ringer's solution andisotonic sodium chloride. The carrier may consists exclusively of anaqueous buffer (“exclusively” means no auxiliary agents or encapsulatingsubstances are present which might affect or mediate uptake of theROS-inhibiting therapeutic). Such substances include, for example,micellar structures, such as liposomes or capsids, as described below.Aqueous suspensions may include suspending agents such as cellulosederivatives, sodium alginate, polyvinyl-pyrrolidone and gum tragacanth,and a wetting agent such as lecithin. Suitable preservatives for aqueoussuspensions include ethyl and n-propyl p-hydroxybenzoate.

ROS kinase-inhibiting therapeutic compositions may also includeencapsulated formulations to protect the therapeutic (e.g. a dsRNAcompound) against rapid elimination from the body, such as a controlledrelease formulation, including implants and microencapsulated deliverysystems. Biodegradable, biocompatible polymers can be used, such asethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen,polyorthoesters, and polylactic acid. Methods for preparation of suchformulations will be apparent to those skilled in the art. The materialscan also be obtained commercially from Alza Corporation and NovaPharmaceuticals, Inc. Liposomal suspensions (including liposomestargeted to infected cells with monoclonal antibodies to viral antigens)can also be used as pharmaceutically acceptable carriers. These can beprepared according to methods known to those skilled in the art, forexample, as described in U.S. Pat. No. 4,522,811: PCT publication WO91/06309; and European patent publication EP-A-43075. An encapsulatedformulation may comprise a viral coat protein. The viral coat proteinmay be derived from or associated with a virus, such as a polyoma virus,or it may be partially or entirely artificial. For example, the coatprotein may be a Virus Protein 1 and/or Virus Protein 2 of the polyomavirus, or a derivative thereof.

ROS-inhibiting compositions can also comprise a delivery vehicle,including liposomes, for administration to a subject, carriers anddiluents and their salts, and/or can be present in pharmaceuticallyacceptable formulations. For example, methods for the delivery ofnucleic acid molecules are described in Akhtar et al., 1992, Trends CellBio., 2, 139; DELIVERY STRATEGIES FOR ANTISENSE OLIGONUCLEOTIDETHERAPEUTICS, ed. Akbtar, 1995, Maurer et al., 1999, Mol. Membr. Biol.,16, 129-140; Hofland and Huang, 1999, Handb. Exp. Pharmacol., 137,165-192; and Lee et al., 2000, ACS Symp. Ser., 752, 184-192. Beigelmanet al., U.S. Pat. No. 6,395,713 and Sullivan et al., PCT WO 94/02595further describe the general methods for delivery of nucleic acidmolecules. These protocols can be utilized for the delivery of virtuallyany nucleic acid molecule.

ROS-inhibiting therapeutics can be administered to a mammalian tumor bya variety of methods known to those of skill in the art, including, butnot restricted to, encapsulation in liposomes, by iontophoresis, or byincorporation into other vehicles, such as hydrogels, cyclodextrins,biodegradable nanocapsules, and bioadhesive microspheres, or byproteinaceous vectors (O'Hare and Normand, International PCT PublicationNo. WO 00/53722). Alternatively, the therapeutic/vehicle combination islocally delivered by direct injection or by use of an infusion pump.Direct injection of the composition, whether subcutaneous,intramuscular, or intradermal, can take place using standard needle andsyringe methodologies, or by needle-free technologies such as thosedescribed in Conry et al., 1999, Clin. Cancer Res., 5, 2330-2337 andBarry et al., International PCT Publication No. WO 99/3 1262.

Pharmaceutically acceptable formulations of ROS kinase-inhibitorytherapeutics include salts of the above described compounds, e.g., acidaddition salts, for example, salts of hydrochloric, hydrobromic, aceticacid, and benzene sulfonic acid. A pharmacological composition orformulation refers to a composition or formulation in a form suitablefor administration, e.g., systemic administration, into a cell orpatient, including for example a human. Suitable forms, in part, dependupon the use or the route of entry, for example oral, transdermal, or byinjection. Such forms should not prevent the composition or formulationfrom reaching a target cell. For example, pharmacological compositionsinjected into the blood stream should be soluble. Other factors areknown in the art, and include considerations such as toxicity and formsthat prevent the composition or formulation from exerting its effect.

Administration routes that lead to systemic absorption (i.e. systemicabsorption or accumulation of drugs in the blood stream followed bydistribution throughout the entire body), are desirable and include,without limitation: intravenous, subcutaneous, intraperitoneal,inhalation, oral, intrapulmonary and intramuscular. Each of theseadministration routes exposes the ROS-inhibiting therapeutic to anaccessible diseased tissue or tumor. The rate of entry of a drug intothe circulation has been shown to be a function of molecular weight orsize. The use of a liposome or other drug carrier comprising thecompounds of the instant invention can potentially localize the drug,for example, in certain tissue types, such as the tissues of thereticular endothelial system (RES). A liposome formulation that canfacilitate the association of drug with the surface of cells, such as,lymphocytes and macrophages is also useful. This approach can provideenhanced delivery of the drug to target cells by taking advantage of thespecificity of macrophage and lymphocyte immune recognition of abnormalcells, such as cancer cells.

By “pharmaceutically acceptable formulation” is meant, a composition orformulation that allows for the effective distribution of the nucleicacid molecules of the instant invention in the physical location mostsuitable for their desired activity. Nonlimiting examples of agentssuitable for formulation with the nucleic acid molecules of the instantinvention include: P-glycoprotein inhibitors (such as Pluronic P85),which can enhance entry of drugs into the CNS (Jolliet-Riant andTillement, 1999, Fundam. Clin. Pharmacol., 13, 16-26); biodegradablepolymers, such as poly (DL-lactide-coglycolide) microspheres forsustained release delivery after intracerebral implantation (Emerich etal, 1999, Cell Transplant, 8, 47-58) (Alkermes, Inc. Cambridge, Mass.);and loaded nanoparticles, such as those made of polybutylcyanoacrylate,which can deliver drugs across the blood brain barrier and can alterneuronal uptake mechanisms (Prog Neuro-psychopharmacol Biol Psychiatry,23, 941-949, 1999). Other non-limiting examples of delivery strategiesfor the ROS-inhibiting compounds useful in the method of the inventioninclude material described in Boado et al., 1998, J. Pharm. Sci., 87,1308-1315; Tyler et al., 1999, FEBS Lett., 421, 280-284; Pardridge etal., 1995, PNAS USA., 92, 5592-5596; Boado, 1995, Adv. Drug Deliver,Rev., 15, 73-107; Aldrian-Herrada et al., 1998, Nucleic Acids Res., 26,4910-4916; and Tyler et al., 1999, PNAS USA., 96, 7053-7058.

Therapeutic compositions comprising surface-modified liposomescontaining poly (ethylene glycol) lipids (PEG-modified, orlong-circulating liposomes or stealth liposomes) may also be suitablyemployed in the methods of the invention. These formulations offer amethod for increasing the accumulation of drugs in target tissues. Thisclass of drug carriers resists opsonization and elimination by themononuclear phagocytic system (MPS or RES), thereby enabling longerblood circulation times and enhanced tissue exposure for theencapsulated drug (Lasic et al. Chem. Rev. 1995, 95, 2601-2627; Ishiwataet al., Chem. Pharm. Bull. 1995, 43, 1005-1011). Such liposomes havebeen shown to accumulate selectively in tumors, presumably byextravasation and capture in the neovascularized target tissues (Lasicet al., Science 1995, 267, 1275-1276; Oku et al., 1995, Biochim.Biophys. Acta. 1238, 86-90). The long-circulating liposomes enhance thepharmacokinetics and pharmacodynamics of DNA and RNA, particularlycompared to conventional cationic liposomes which are known toaccumulate in tissues of the MPS (Liu et al., J. Biol. Chem. 1995, 42,24864-24870; Choi et al., International PCT Publication No. WO 96/10391;Ansell et al., International PCT Publication No. WO 96/10390: Holland etal., International PCT Publication No. WO 96/10392). Long-circulatingliposomes are also likely to protect drugs from nuclease degradation toa greater extent compared to cationic liposomes, based on their abilityto avoid accumulation in metabolically aggressive MPS tissues such asthe liver and spleen.

Therapeutic compositions may include a pharmaceutically effective amountof the desired compounds in a pharmaceutically acceptable carrier ordiluent. Acceptable carriers or diluents for therapeutic use are wellknown in the pharmaceutical art, and are described, for example, inREMINGTON'S PHARMACEUTICAL SCIENCES, Mack Publishing Co. (A. R. Gennaroedit. 1985). For example, preservatives, stabilizers, dyes and flavoringagents can be provided. These include sodium benzoate, sorbic acid andesters of p-hydroxybenzoic acid. In addition, antioxidants andsuspending agents can be used.

A pharmaceutically effective dose is that dose required to prevent,inhibit the occurrence, or treat (alleviate a symptom to some extent,preferably all of the symptoms) of a disease state. The pharmaceuticallyeffective dose depends on the type of disease, the composition used, theroute of administration, the type of mammal being treated, the physicalcharacteristics of the specific mammal under consideration, concurrentmedication, and other factors that those skilled in the medical artswill recognize. Generally, an amount between 0.1 mg/kg and 100 mg/kgbody weight/day of active ingredients is administered dependent uponpotency of the negatively charged polymer.

Dosage levels of the order of from about 0.1 mg to about 140 mg perkilogram of body weight per day are useful in the treatment of theabove-indicated conditions (about 0.5 mg to about 7 g per patient perday). The amount of active ingredient that can be combined with thecarrier materials to produce a single dosage form varies depending uponthe host treated and the particular mode of administration. Dosage unitforms generally contain between from about 1 mg to about 500 mg of anactive ingredient. It is understood that the specific dose level for anyparticular patient depends upon a variety of factors including theactivity of the specific compound employed, the age, body weight,general health, sex, diet, time of administration, route ofadministration, and rate of excretion, drug combination and the severityof the particular disease undergoing therapy.

For administration to non-human animals, the composition can also beadded to the animal feed or drinking water. It can be convenient toformulate the animal feed and drinking water compositions so that theanimal takes in a therapeutically appropriate quantity of thecomposition along with its diet. It can also be convenient to presentthe composition as a premix for addition to the feed or drinking water.

A ROS-inhibiting therapeutic useful in the practice of the invention maycomprise a single compound as described above, or a combination ofmultiple compounds, whether in the same class of inhibitor (i.e.antibody inhibitor), or in different classes (i.e antibody inhibitorsand small-molecule inhibitors). Such combination of compounds mayincrease the overall therapeutic effect in inhibiting the progression ofa fusion protein-expressing cancer. For example, the therapeuticcomposition may a small molecule inhibitor, such as STI-571 (Gleevec®)alone, or in combination with other Gleevec® analogues targeting ROSactivity and/or small molecule inhibitors of EGFR, such as Tarceva™ orIressa™. The therapeutic composition may also comprise one or morenon-specific chemotherapeutic agent in addition to one or more targetedinhibitors. Such combinations have recently been shown to provide asynergistic tumor killing effect in many cancers. The effectiveness ofsuch combinations in inhibiting ROS activity and tumor growth in vivecan be assessed as described below.

Identification of Mutant ROS Kinase-Inhibiting Compounds.

The invention also provides, in part, a method for determining whether acompound inhibits the progression of a cancer characterized by aCD74-ROS translocation and/or fusion polypeptide, by determining whetherthe compound inhibits the activity of CD74-ROS fusion polypeptide in thecancer. In some preferred embodiments, inhibition of activity of ROS isdetermined by examining a biological sample comprising cells from bonemarrow, blood, or a tumor. In another preferred embodiment, inhibitionof activity of ROS is determined using at least one mutant ROSpolynucleotide or polypeptide-specific reagent of the invention.

The tested compound may be any type of therapeutic or composition asdescribed above. Methods for assessing the efficacy of a compound, bothin vitro and in vivo, are well established and known in the art. Forexample, a composition may be tested for ability to inhibit ROS in vitrousing a cell or cell extract in which ROS kinase is activated. A panelof compounds may be employed to test the specificity of the compound forROS (as opposed to other targets, such as EGFR or PDGFR).

Another technique for drug screening which may be used provides for highthroughput screening of compounds having suitable binding affinity to aprotein of interest, as described in published PCT applicationWO84/03564. In this method, as applied to mutant ROS polypeptides, largenumbers of different small test compounds are synthesized on a solidsubstrate, such as plastic pins or some other surface. The testcompounds are reacted with mutant ROS polypeptide, or fragments thereof,and washed. Bound mutant polypeptide (e.g. CD74-ROS fusion polypeptide)is then detected by methods well known in the art. Purified mutant ROSpolypeptide can also be coated directly onto plates for use in theaforementioned drug screening techniques. Alternatively,non-neutralizing antibodies can be used to capture the peptide andimmobilize it on a solid support.

A compound found to be an effective inhibitor of ROS activity in vitromay then be examined for its ability to inhibit the progression of acancer expressing CD74-ROS fusion polypeptide, in vivo, using, forexample, mammalian xenografts harboring human NSCLC tumors that aredriven by CD74-ROS fusion protein. In this procedure, cell lines knownto be driven by CD74-ROS fusion protein are placed subcutaneously in themouse. The cells then grow into a tumor mass that may be visuallymonitored. The mouse may then be treated with the drug. The effect ofthe drug treatment on tumor size may be externally observed. The mouseis then sacrificed and the tumor removed for analysis by IHC and Westernblot. Similarly, mammalian bone marrow transplants may be prepared, bystandard methods, to examine drug response in hematological tumorsexpressing a mutant ROS kinase. In this way, the effects of the drug maybe observed in a biological setting most closely resembling a patient.The drug's ability to alter signaling in the tumor cells or surroundingstromal cells may be determined by analysis withphosphorylation-specific antibodies. The drug's effectiveness ininducing cell death or inhibition of cell proliferation may also beobserved by analysis with apoptosis specific markers such as cleavedcaspase 3 and cleaved PARP.

Toxicity and therapeutic efficacy of such compounds can be determined bystandard pharmaceutical procedures in cell cultures or experimentalanimals, e.g., for determining the LD50 (the dose lethal to 50% of thepopulation) and the ED50 (the dose therapeutically effective in 50% ofthe population). The dose ratio between toxic and therapeutic effects isthe therapeutic index and it can be expressed as the ratio LD50/ED50.Compounds which exhibit high therapeutic indices are preferred.

The teachings of all references cited above and below are herebyincorporated herein by reference. The following Examples are providedonly to further illustrate the invention, and are not intended to limitits scope, except as provided in the claims appended hereto. The presentinvention encompasses modifications and variations of the methods taughtherein which would be obvious to one of ordinary skill in the art.

Example 1 Identification of ROS Kinase Activity from NSCLC Patients byGlobal Phosphopeptide Profiling

The global phosphorylation profile of kinase activation in several humanNSCLC patients, including CS042, were examined using a recentlydescribed and powerful technique for the isolation and massspectrometric characterization of modified peptides from complexmixtures (the “IAP” technique, see Rush et al., supra). The IAPtechnique was performed using a phosphotyrosine-specific antibody (CELLSIGNALING TECHNOLOGY, INC., Beverly, Mass., 2003/04 Cat. #9411) toisolate, and subsequently characterize, phosphotyrosine-containingpeptides from extracts of the NSCLC cell lines.

Specifically, the IAP approach was employed go facilitate theidentification of activated tyrosine kinases in the NSCLC patients, inorder to identify novel drivers of this disease.

Phosphopeptide Immunoprecipitation.

A total of 0.5 g tumor tissue was homogenized and lysed in urea lysisbuffer (20 mM HEPES pH 8.0, 9M urea, 1 mM sodium vanadate, 2.5 mM sodiumpyrophosphate, 1 mM beta-glycerophosphate) at 1.25×10⁸ cells/ml andsonicated. Sonicated lysates were cleared by centrifugation at 20,000×g,and proteins were reduced and alkylated as described previously (seeRush et al., Nat. Biotechnol. 23(1): 94-101 (2005)). Samples werediluted with 20 mM HEPES pH 8.0 to a final urea concentration of 2M.Trypsin (1 mg/ml in 0.001 M HCl) was added to the clarified lysate at1:100 v/v. Samples were digested overnight at room temperature.

Following digestion, lysates were acidified to a final concentration of1% TFA. Peptide purification was carried out using Sep-Pak C₁₈ columnsas described previously (see Rush et al., supra.). Followingpurification, all elutions (8%, 12%, 15%, 18%, 22%, 25%, 30/%, 35% and40% acetonitrile in 0.1% TFA) were combined and lyophilized. Driedpeptides were resuspended in 1.4 ml MOPS buffer (50 mM MOPS/NaOH pH 7.2,10 mM Na₂HPO₄, 50 mM NaCl) and insoluble material removed bycentrifugation at 12,000×g for 10 minutes.

The phosphotyrosine monoclonal antibody P-Tyr-100 (Cell SignalingTechnology) from ascites fluid was coupled non-covalently to protein Gagarose beads (Roche) at 4 mg/ml beads overnight at 4° C. Aftercoupling, antibody-resin was washed twice with PBS and three times withMOPS buffer. Immobilized antibody (40 μl, 160 μg) was added as a 1:1slurry in MOPS IP buffer to the solubilized peptide fraction, and themixture was incubated overnight at 4° C. The immobilized antibody beadswere washed three times with MOPS buffer and twice with ddH₂O. Peptideswere eluted twice from beads by incubation with 40 μl of 0.1% TFA for 20minutes each, and the fractions were combined.

Analysis by LC-MS/MS Mass Spectrometry.

Peptides in the IP eluate (40 μl) were concentrated and separated fromeluted antibody using Stop and Go extraction tips (StageTips) (seeRappsilber et al., Anal. Chem., 75(3): 663-70 (2003)). Peptides wereeluted from the microcolumns with 1 μl of 60% MeCN, 0.1% TFA into 7.6 μlof 0.4% acetic acid/0.005% heptafluorobutyric acid (HFBA). The samplewas loaded onto a 10 cm×75 μm PicoFrit capillary column (New Objective)packed with Magic C18 AQ reversed-phase resin (Michrom Bioresources)using a Famos autosampler with an inert sample injection valve (Dionex).The column was developed with a 45-min linear gradient of acetonitrilein 0.4% acetic acid, 0.005% HFBA delivered at 280 nl/min (Ultimate,Dionex).

Tandem mass spectra were collected in a data-dependent manner with anLCQ Deca XP Plus ion trap mass spectrometer (ThermoFinnigan), using atop-four method, a dynamic exclusion repeat count of 1, and a repeatduration of 0.5 min.

Database Analysis & Assignments.

MS/MS spectra were evaluated using TurboSequest (ThermoFinnigan) (in theSequest Browser package (v. 27, rev. 12) supplied as part of BioWorks3.0). Individual MS/MS spectra were extracted from the raw data fileusing the Sequest Browser program CreateDta, with the followingsettings: bottom MW, 700; top MW, 4.500; minimum number of ions, 20;minimum TIC, 4×10⁵; and precursor charge state, unspecified. Spectrawere extracted from the beginning of the raw data file before sampleinjection to the end of the eluting gradient. The IonQuest and VuDtaprograms were not used to further select MS/MS spectra for Sequestanalysis. MS/MS spectra were evaluated with the following TurboSequestparameters: peptide mass tolerance, 2.5; fragment ion tolerance, 0.0;maximum number of differential amino acids per modification, 4: masstype parent, average; mass type fragment, average; maximum number ofinternal cleavage sites, 10; neutral losses of water and ammonia from band y ions were considered in the correlation analysis. Proteolyticenzyme was specified except for spectra collected from elastase digests.

Searches were done against the NCBI human database released on Aug. 24,2004 containing 27,175 proteins allowing oxidized methionine (M+16) andphosphorylation (Y+80) as dynamic modifications.

In proteomics research, it is desirable to validate proteinidentifications based solely on the observation of a single peptide inone experimental result, in order to indicate that the protein is, infact, present in a sample. This has led to the development ofstatistical methods for validating peptide assignments, which are notyet universally accepted, and guidelines for the publication of proteinand peptide identification results (see Carr et al., Mol. CellProteomics 3: 531-533 (2004)), which were followed in this Example.However, because the immunoaffinity strategy separates phosphorylatedpeptides from unphosphorylated peptides, observing just onephosphopeptide from a protein is a common result, since manyphosphorylated proteins have only one tyrosine-phosphorylated site.

For this reason, it is appropriate to use additional criteria tovalidate phosphopeptide assignments. Assignments are likely to becorrect if any of these additional criteria are met: (i) the samesequence is assigned to co-eluting ions with different charge states,since the MS/MS spectrum changes markedly with charge state; (ii) thesite is found in more than one peptide sequence context due to sequenceoverlaps from incomplete proteolysis or use of proteases other thantrypsin; (iii) the site is found in more than one peptide sequencecontext due to homologous but not identical protein isoforms: (iv) thesite is found in more than one peptide sequence context due tohomologous but not identical proteins among species; and (v) sitesvalidated by MS/MS analysis of synthetic phosphopeptides correspondingto assigned sequences, since the ion trap mass spectrometer produceshighly reproducible MS/MS spectra. The last criterion is routinelyemployed to confirm novel site assignments of particular interest.

All spectra and all sequence assignments made by Sequest were importedinto a relational database. Assigned sequences were accepted or rejectedfollowing a conservative, two-step process. In the first step, a subsetof high-scoring sequence assignments was selected by filtering for XCorrvalues of at least 1.5 for a charge state of +1, 2.2 for +2, and 3.3 for+3, allowing a maximum RSp value of 10. Assignments in this subset wererejected if any of the following criteria were satisfied: (i) thespectrum contained at least one major peak (at least 10% as intense asthe most intense ion in the spectrum) that could not be mapped to theassigned sequence as an a, b, or y ion, as an ion arising fromneutral-loss of water or ammonia from a b or y ion, or as a multiplyprotonated ion; (ii) the spectrum did not contain a series of b or yions equivalent to at least six uninterrupted residues; or (iii) thesequence was not observed at least five times in all the studies we haveconducted (except for overlapping sequences due to incompleteproteolysis or use of proteases other than trypsin). In the second step,assignments with below-threshold scores were accepted if the low-scoringspectrum showed a high degree of similarity to a high-scoring spectrumcollected in another study, which simulates a true referencelibrary-searching strategy. All spectra supporting the final list ofassigned sequences (not shown here) were reviewed by at least threescientists to establish their credibility.

The foregoing IAP analysis identified many tyrosine phosphorylatedproteins, the majority of which are novel. Among tyrosine phosphorylatedkinases were several of those detected are not normally detected by MSanalysis in other NSCLC cell lines (unpublished data), including ROSkinase.

Example 2 Isolation & Sequencing of CD74-ROS Fusion Gene

Given the presence of the activated form of ROS kinase detected in aNSCLC patient, 5′ rapid amplification of cDNA ends on the sequenceencoding the kinase domain of ROS was conducted in order to determinewhether a chimeric ROS transcript was present.

Rapid Amplification of Complementary DNA Ends

RNeasy Mini Kit (Qiagen) was used to extract RNA from CS045 cell line.DNA was extracted with the use of DNeasy Tissue Kit (Qiagen). Rapidamplification of cDNA ends was performed with the use of 5′ RACE system(Invitrogen) with primers ROS-GSP1 for cDNA synthesis and ROS-GSP2 andROS-GSP3 for a nested PCR reaction.

PCR Assay

For RT-PCR, first-strand cDNA was synthesized from 2.5 μg of total RNAwith the use of SuperScript™ III first-strand synthesis system(Invitrogen) with oligo (dT)₂₀. Then, the CD74-ROS fusion gene wasamplified with the use of primer pairs CD74-F1 and ROS-GSP3:

ROS-GSP1: (SEQ ID NO: 7) ACCCTTCTCGGTTCTTCGTTTCCA ROS-GSP2:(SEQ ID NO: 8) GCAGCTCAGCCAACTCTTTGTCTT ROS-GSP3: (SEQ ID NO: 9)TGCCAGACAAAGGTCAGTGGGATT CD74-F1: (SEQ ID NO: 10)GCAGAATGCCACCAAGTATGGCAASequence analysis of the resultant product revealed that the c-terminalof ROS was fused to CD74 gene N-terminus (see FIG. 1, panel B and C).The CD74-ROS fusion gene was in-frame and fused the first 208 aminoacids of CD74 to the last 495 amino acids of ROS (see FIG. 1, panel B),resulting in a fusion protein. CD74 was located on chromosome 5q32,whereas ROS was on chromosome 6q22. Thus, the fusion gene was created byt(5:6)(q32;q22).

The fusion of CD74 and ROS was confirmed by reverse-transcriptase-PCR onRNA. See FIG. 5

Example 3 Detection of CD74-ROS Fusion Protein Expression in a HumanCancer Sample Using FISH Assay

The presence of the CD74-ROS fusion protein in human NSCLC tumor sampleswas detected using a fluorescence in situ hybridization (FISH) assay, aspreviously described. See, e.g., Verma et al. HUMAN CHROMOSOMES: AMANUAL OF BASIC TECHNIQUES, Pergamon Press, New York, N.Y. (1988). Over200 paraffin-embedded human NSCLC tumor samples were examined.

For analyzing rearrangements involving ROS, a dual color break-apartprobe was designed. A proximal probe (BAC clone RP1-179P9) and twodistal probes (BAC clone RP11-323O17, RP1-94G16) were labeled withSpectrum Orange dUTP or Spectrum Green dUTP, respectively. Labeling ofthe probes by nick translation and interphase FISH using FFPE tissuesections were done according to the manufactures instructions (Vysis)with the following modifications. In brief, paraffin embedded tissuesections were re-hydrated and subjected to microwave antigen retrievalin 0.01M Citrate buffer (pH 6.0) for 11 minutes. Sections were digestedwith Protease (4 mg/ml Pepsin, 2000-3000 U/mg) for 25 minutes at 37° C.,dehydrated and hybridized with the FISH probe set at 37° C. for 18hours. After washing, 4′,6-diamidino-2-phenylindole (DAPI; mg/ml) inVectashield mounting medium (Vector Laboratories, Burlingame, Calif.)was applied for nuclear counterstaining.

The ROS rearrangement probe contains two differently labeled probes onopposite sides of the breakpoint of the ROS gene in the wild typesequence (see FIG. 4B and FIG. 1). When hybridized, the native ROSregion will appear as an orange/green fusion signal, while rearrangementat this locus (as occurs in the CD74-ROS fusion protein) will result inseparate orange and green signals.

The FISH analysis revealed a low incidence of this ROS mutation in thesample population studied. Two out of 123 tumors or 1.6% of tumorscontained the fusion mutation. However, given the high incidence ofNSCLC worldwide (over 151,00 new cases in the U.S. annually, alone),there are expected to be a significant number of patients that harborthis mutant ROS, which patients may benefit from a ROS-inhibitingtherapeutic regime.

Example 4 Detection of Mutant ROS Kinase Expression in a Human CancerSample Using PCR Assay

The presence of truncated ROS kinase and/or CD74-ROS fusion protein in ahuman cancer sample may be detected using either genomic or reversetranscriptase (RT) polymerase chain reaction (PCR), previouslydescribed. See, e.g., Cools et al., N. Engl. J. Med. 348: 1201-1214(2003).

Briefly and by way of example, tumor or pleural effusion samples may beobtained from a patient having NSCLC using standard techniques. PCRprobes against truncated ROS kinase or CD74-ROS fusion protein areconstructed. RNeasy Mini Kit (Qiagen) may be used to extract RNA fromthe tumor or pleural effusion samples. DNA may be extracted with the useof DNeasy Tissue Kit (Qiagen). For RT-PCR, first-strand cDNA issynthesized from, e.g., 2.5 μg of total RNA with the use, for example,of SuperScript™ III first-strand synthesis system (Invitrogen) witholigo (dT)₂₀. Then, the CD74-ROS fusion gene is amplified with the useof primer pairs. e.g. CD74-F1 and ROS-GSP3.

Such an analysis will identify a patient having a cancer characterizedby expression of the truncated ROS kinase (and/or CD74-ROS fusionprotein), which patient is a candidate for treatment using aROS-inhibiting therapeutic.

What is claimed is:
 1. An isolated polynucleotide comprising anucleotide sequence at least 95% identical to a sequence selected fromthe group consisting of: (a) a nucleotide sequence encoding a CD74-ROSfusion polypeptide comprising the amino acid sequence of SEQ ID NO: 1;(b) a nucleotide sequence encoding a CD74-ROS fusion polypeptide, saidnucleotide sequence comprising the nucleotide sequence of SEQ ID NO: 2;(c) a nucleotide sequence encoding a CD74-ROS fusion polypeptidecomprising the N-terminal amino acid sequence of CD74 (residues 1-208 ofSEQ ID NO: 3) and the kinase domain of ROS (residues 1945-2222 of SEQ IDNO: 5); (d) a nucleotide sequence comprising the N-terminal nucleotidesequence of CD74 (residues 1-624 of SEQ ID NO: 4) and the kinase domainnucleotide sequence of ROS (residues 6032-6865 of SEQ ID NO: 6); (e) anucleotide sequence comprising at least six contiguous nucleotidesencompassing the fusion junction (residues 622-627 of SEQ ID NO: 2) of aCD74-ROS fusion polynucleotide; (f) a nucleotide sequence encoding apolypeptide comprising at least six contiguous amino acids encompassingthe fusion junction (residues 208-209 of SEQ ID NO: 1) of a CD74-ROSfusion polypeptide; and (g) a nucleotide sequence complementary to anyof the nucleotide sequences of (a)-(f).
 2. The isolated polynucleotideof claim 1, wherein said nucleotide sequence of (b) comprises the codingnucleotide sequence of the cDNA clone contained in ATCC Deposit No.______.
 3. An isolated polynucleotide that hybridizes under stringenthybridization conditions to a polynucleotide of claim 1, wherein saidisolated polynucleotide that hybridizes does not hybridize understringent hybridization conditions to a polynucleotide having anucleotide sequence consisting of only A residues or of only T residues.4. The isolated polynucleotide of claim 3, wherein said polynucleotidefurther comprises a detectable label.
 5. A method for producing arecombinant vector comprising inserting an isolated nucleic acidmolecule of claim 1 into a vector.
 6. A recombinant vector produced bythe method of claim
 5. 7. A method for making a recombinant host cellcomprising introducing the recombinant vector of claim 6 into a hostcell.
 8. A recombinant host cell produced by the method of claim
 7. 9. Amethod for producing a recombinant CD74-ROS fusion polypeptide, saidmethod comprising culturing the recombinant host cell of claim 8 underconditions suitable for the expression of said fusion polypeptide andrecovering said polypeptide.
 10. An isolated polypeptide comprising anamino acid sequence at least 95% identical to a sequence selected fromthe group consisting of: (a) an amino acid sequence encoding a CD74-ROSfusion polypeptide comprising the amino acid sequence of SEQ ID NO: 1;(b) an amino acid sequence encoding a CD74-ROS fusion polypeptidecomprising the N-terminal amino acid sequence of CD74 (residues 1-208 ofSEQ ID NO: 3) and the kinase domain of ROS (residues 1945-2222 of SEQ IDNO: 5); and (c) an amino acid sequence encoding a polypeptide comprisingat least six contiguous amino acids encompassing the fusion junction(residues 208-209 of SEQ ID NO: 1) of a CD74-ROS fusion polypeptide. 11.The isolated polypeptide of claim 10, wherein said amino acid sequenceof (a) comprises the CD74-ROS fusion polypeptide sequence encoded by thecDNA contained in ATCC Deposit No. ______.
 12. A recombinant CD74-ROSfusion polypeptide or truncated ROS kinase polypeptide produced usingthe recombinant vector of claim 6 or the recombinant host cell of claim8.
 13. An isolated reagent that specifically binds to or detects aCD74-ROS fusion polypeptide of claim 10, but does not bind to or detecteither wild type CD74 or wild type ROS.
 14. The isolated reagent ofclaim 12, wherein said reagent is an antibody or a heavy-isotope labeled(AQUA) peptide.
 15. The heavy isotope labeled (AQUA) peptide of claim15, wherein said peptide comprises the amino acid sequence of the fusionjunction of CD74-ROS fusion polypeptide.
 16. A method for detecting thepresence of a mutant ROS polynucleotide and/or polypeptide in a cancer,said method comprising the steps of: (a) obtaining a biological samplefrom a patient having or suspected of having cancer; and (b) utilizingat least one reagent that detects a polynucleotide of claim 1 and/or atleast one reagent of claim 13 to determine whether a CD74-ROS fusionpolynucleotide and/or polypeptide is present in said biological sample.17. The method of claim 16, wherein said cancer is lung cancer.
 18. Themethod of claim 17, wherein said lung cancer is non-small cell lungcarcinoma (NSCLC).
 19. The method of claim 17, wherein the presence of amutant ROS polynucleotide or polypeptide identifies a cancer that islikely to respond to a composition comprising at least one ROSkinase-inhibiting therapeutic.
 20. The method of claim 17, wherein themethod is implemented in a flow-cytometry (FC), immuno-histochemistry(IHC), or immuno-fluorescence (IF) assay format.
 21. The method of claim17, wherein the method is implemented in a fluorescence in situhybridization (FISH) or polymerase chain reaction (PCR) assay format.22. The method of claim 17, wherein the activity of said CD74-ROS fusionpolypeptide is detected.
 23. A method for determining whether a compoundinhibits the progression of a cancer characterized by a CD74-ROS fusionpolynucleotide and/or polypeptide, said method comprising the step ofdetermining whether said compound inhibits the expression and/oractivity of said CD74-ROS fusion polypeptide in said cancer.
 24. Themethod of claim 23, wherein inhibition of expression and/or activity ofsaid CD74-ROS fusion polypeptide is determined using at least onereagent that detects a polynucleotide of claim 1 and/or at least onereagent of claim
 13. 25. A method for inhibiting the progression of acancer that expresses a CD74-ROS fusion polypeptide, said methodcomprising the step of inhibiting the expression and/or activity of saidCD74-ROS fusion polypeptide in said cancer.
 26. The method of claim 25,wherein said cancer is lung cancer.
 27. The method of claim 26, whereinsaid lung cancer is non-small cell lung carcinoma (NSCLC).
 28. A kit forthe detection of a CD74-ROS fusion polynucleotide and/or polypeptide ina biological sample, said kit comprising at least one polynucleotide ofclaim 1 and/or at least one reagent of claim 13, and one or moresecondary reagents.